From 4773bd73baea9a721d23627ae4ba01a5dd9c0662 Mon Sep 17 00:00:00 2001 From: rmgpanw <54263156+rmgpanw@users.noreply.github.com> Date: Mon, 23 Sep 2024 09:08:21 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20rmgpanw/?= =?UTF-8?q?gtexr@44fdac59118e94209bc7ce3735e57941a1ef087a=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- index.html | 2 ++ pkgdown.yml | 2 +- ...te_expression_quantitative_trait_loci.html | 20 +++++++++---------- search.json | 2 +- 4 files changed, 14 insertions(+), 12 deletions(-) diff --git a/index.html b/index.html index 6de885e..e728407 100644 --- a/index.html +++ b/index.html @@ -192,6 +192,8 @@

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    • diff --git a/pkgdown.yml b/pkgdown.yml index 981e3f8..ac75d53 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: developer_guide: developer_guide.html gtexr: gtexr.html -last_built: 2024-09-20T06:42Z +last_built: 2024-09-23T09:07Z urls: reference: https://rmgpanw.github.io/gtexr/reference article: https://rmgpanw.github.io/gtexr/articles diff --git a/reference/calculate_expression_quantitative_trait_loci.html b/reference/calculate_expression_quantitative_trait_loci.html index 2551b28..91fd980 100644 --- a/reference/calculate_expression_quantitative_trait_loci.html +++ b/reference/calculate_expression_quantitative_trait_loci.html @@ -132,16 +132,16 @@

    Examples#> # A tibble: 670 × 15 #> data error gencodeId geneSymbol genotypes hetCount homoAltCount #> <dbl> <dbl> <chr> <chr> <int> <int> <int> -#> 1 -0.175 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 2 -0.247 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 3 -1.27 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 4 -1.53 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 5 0.263 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 6 0.0467 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 7 -1.42 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 8 -1.88 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 9 1.42 0.148 ENSG00000203782.5 LOR 0 38 0 -#> 10 1.98 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 1 -1.16 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 2 0.978 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 3 0.0542 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 4 -0.278 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 5 0.182 0.148 ENSG00000203782.5 LOR 1 38 0 +#> 6 -0.614 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 7 0.462 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 8 -0.125 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 9 0.421 0.148 ENSG00000203782.5 LOR 0 38 0 +#> 10 0.274 0.148 ENSG00000203782.5 LOR 0 38 0 #> # ℹ 660 more rows #> # ℹ 8 more variables: homoRefCount <int>, maf <dbl>, nes <dbl>, pValue <dbl>, #> # pValueThreshold <dbl>, tStatistic <dbl>, tissueSiteDetailId <chr>, diff --git a/search.json b/search.json index d06f53d..32b14a0 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://rmgpanw.github.io/gtexr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 gtexr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/developer_guide.html","id":"functions","dir":"Articles","previous_headings":"","what":"Functions","title":"Developer guide","text":"Function name title API endpoint lower case, words separated underscores. @description section copied verbatim API documentation site ends link corresponding API endpoint documentation. notes may added @details. Names match API endpoint, except argument accepts array (vector R) values, case pluralised.1 Default values also match API endpoint. Query parameters flagged “required” GTEx Portal API documentation default values.2 documented gtexr_arguments.R. functions therefore use @inheritParams gtexr_arguments documentation. Use @family roxygen tag match categories API documentation. used categorise functions pkgdown site reference page. Return tibble. first example @examples must produce output single function call without assignment (e.g. get_news_items(), x <- get_news_items()). used pre-populate argument values gtexr shiny app working example. examples surrounded \\dontrun{}.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"shiny-app","dir":"Articles","previous_headings":"","what":"Shiny app","title":"Introduction to gtexr","text":"Users can try functions interatively ⭐gtexr shiny app⭐, pre-populates query parameters first working example function’s documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"Introduction to gtexr","text":"rest vignette outlines example applications gtexr.","code":"library(gtexr) library(dplyr) library(purrr)"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-build-37-coordinates-for-a-variant","dir":"Articles","previous_headings":"Examples","what":"Get build 37 coordinates for a variant","title":"Introduction to gtexr","text":"","code":"get_variant(snpId = \"rs1410858\") |> tidyr::separate( col = b37VariantId, into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\", remove = FALSE ) |> select(snpId:genome_build) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #> snpId b37VariantId chromosome position reference_allele alternative_allele #> #> 1 rs1410858 1_153182116… 1 1531821… C A #> # ℹ 1 more variable: genome_build "},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-gene-symbol-to-versioned-gencode-id","dir":"Articles","previous_headings":"Examples","what":"Convert gene symbol to versioned GENCODE ID","title":"Introduction to gtexr","text":"Use get_gene() get_genes()","code":"get_genes(\"CRP\") |> select(geneSymbol, gencodeId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #> geneSymbol gencodeId #> #> 1 CRP ENSG00000132693.12"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-rsid-to-gtex-variant-id","dir":"Articles","previous_headings":"Examples","what":"Convert rsID to GTEx variant ID","title":"Introduction to gtexr","text":"Use get_variant()","code":"get_variant(snpId = \"rs1410858\") |> select(snpId, variantId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #> snpId variantId #> #> 1 rs1410858 chr1_153209640_C_A_b38"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"for-a-gene-of-interest-which-tissues-have-significant-cis-eqtls","dir":"Articles","previous_headings":"Examples","what":"For a gene of interest, which tissues have significant cis-eQTLs?","title":"Introduction to gtexr","text":"Use get_significant_single_tissue_eqtls() (note requires versioned GENCODE IDs)","code":"gene_symbol_of_interest <- \"CRP\" gene_gencodeId_of_interest <- get_genes(gene_symbol_of_interest) |> pull(gencodeId) |> suppressMessages() gene_gencodeId_of_interest |> get_significant_single_tissue_eqtls() |> distinct(geneSymbol, gencodeId, tissueSiteDetailId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 93 #> # A tibble: 3 × 3 #> geneSymbol gencodeId tissueSiteDetailId #> #> 1 CRP ENSG00000132693.12 Thyroid #> 2 CRP ENSG00000132693.12 Esophagus_Gastroesophageal_Junction #> 3 CRP ENSG00000132693.12 Muscle_Skeletal"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-data-for-non-eqtl-variants","dir":"Articles","previous_headings":"Examples","what":"Get data for non-eQTL variants","title":"Introduction to gtexr","text":"analyses (e.g. Mendelian randomisation) require data variants may may significant eQTLs. Use calculate_expression_quantitative_trait_loci() purrr::map() retrieve data multiple variants","code":"variants_of_interest <- c(\"rs12119111\", \"rs6605071\", \"rs1053870\") variants_of_interest |> set_names() |> map( \\(x) calculate_expression_quantitative_trait_loci( tissueSiteDetailId = \"Liver\", gencodeId = \"ENSG00000237973.1\", variantId = x ) ) |> bind_rows(.id = \"rsid\") |> # optionally, reformat output - first extract genomic coordinates and alleles tidyr::separate( col = \"variantId\", into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\" ) |> # ...then ascertain alternative_allele frequency mutate( alt_allele_count = (2 * homoAltCount) + hetCount, total_allele_count = 2 * (homoAltCount + hetCount + homoRefCount), alternative_allele_frequency = alt_allele_count / total_allele_count ) |> select( rsid, beta = nes, se = error, pValue, minor_allele_frequency = maf, alternative_allele_frequency, chromosome:genome_build, tissueSiteDetailId ) #> # A tibble: 3 × 12 #> rsid beta se pValue minor_allele_frequency alternative_allele_f…¹ #> #> 1 rs121191… 0.0270 0.0670 6.88e-1 0.365 0.635 #> 2 rs6605071 -0.601 0.166 3.88e-4 0.0409 0.959 #> 3 rs1053870 0.0247 0.0738 7.38e-1 0.214 0.214 #> # ℹ abbreviated name: ¹​alternative_allele_frequency #> # ℹ 6 more variables: chromosome , position , reference_allele , #> # alternative_allele , genome_build , tissueSiteDetailId "},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alasdair Warwick. Author, maintainer, copyright holder. Benjamin Zuckerman. Author. Abraham Olvera-Barrios. Author. Chuin Ying Ung. Author. Robert Luben. Author.","code":""},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Warwick , Zuckerman B, Olvera-Barrios , Ung C, Luben R (2024). gtexr: Query GTEx Portal API. R package version 0.1.0.9000, https://github.com/rmgpanw/gtexr, https://rmgpanw.github.io/gtexr/.","code":"@Manual{, title = {gtexr: Query the GTEx Portal API}, author = {Alasdair Warwick and Benjamin Zuckerman and Abraham Olvera-Barrios and Chuin Ying Ung and Robert Luben}, year = {2024}, note = {R package version 0.1.0.9000, https://github.com/rmgpanw/gtexr}, url = {https://rmgpanw.github.io/gtexr/}, }"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"gtexr-","dir":"","previous_headings":"","what":"Query the GTEx Portal API","title":"Query the GTEx Portal API","text":"goal gtexr provide convenient R interface GTEx Portal API V2. New R? Try ⭐shiny app⭐.","code":""},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Query the GTEx Portal API","text":"can install package CRAN: can install development version gtexr GitHub :","code":"install.packages(\"gtexr\") # install.packages(\"devtools\") devtools::install_github(\"rmgpanw/gtexr\")"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Query the GTEx Portal API","text":"Get general information GTEx service: Retrieve eQTL genes whole blood tissue: Retrieve significant eQTLs one genes:","code":"library(gtexr) get_service_info() #> # A tibble: 1 × 9 #> id name version organization_name organization_url description contactUrl #> #> 1 org.g… GTEx… 2.0.0 GTEx Project https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl , environment get_eqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (12360) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 50 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 12360 #> # A tibble: 250 × 10 #> tissueSiteDetailId ontologyId datasetId empiricalPValue gencodeId geneSymbol #> #> 1 Whole_Blood UBERON:001… gtex_v8 1.05e- 9 ENSG0000… WASH7P #> 2 Whole_Blood UBERON:001… gtex_v8 1.06e-25 ENSG0000… RP11-34P1… #> 3 Whole_Blood UBERON:001… gtex_v8 6.31e- 2 ENSG0000… CICP27 #> 4 Whole_Blood UBERON:001… gtex_v8 8.71e- 9 ENSG0000… RP11-34P1… #> 5 Whole_Blood UBERON:001… gtex_v8 6.01e-20 ENSG0000… RP11-34P1… #> 6 Whole_Blood UBERON:001… gtex_v8 6.96e- 9 ENSG0000… RP11-34P1… #> 7 Whole_Blood UBERON:001… gtex_v8 3.10e- 4 ENSG0000… RP11-34P1… #> 8 Whole_Blood UBERON:001… gtex_v8 1.92e- 3 ENSG0000… ABC7-4304… #> 9 Whole_Blood UBERON:001… gtex_v8 1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood UBERON:001… gtex_v8 7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange , pValue , #> # pValueThreshold , qValue get_significant_single_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs12128960 159343657 RS12128960 chr1_1593… CRP 8.52e-5 CRP #> 2 rs12132451 159344052 RS12132451 chr1_1593… CRP 7.92e-5 CRP #> 3 rs12136402 159347493 RS12136402 chr1_1593… CRP 7.92e-5 CRP #> 4 rs10908709 159350390 RS10908709 chr1_1593… CRP 7.92e-5 CRP #> 5 rs10908710 159351189 RS10908710 chr1_1593… CRP 7.92e-5 CRP #> 6 rs11265178 159359256 RS11265178 chr1_1593… CRP 9.62e-5 CRP #> 7 rs35532309 159360755 RS35532309 chr1_1593… CRP 6.11e-5 CRP #> 8 rs6692378 159369451 RS6692378 chr1_1593… CRP 1.17e-6 CRP #> 9 rs10908714 159370563 RS10908714 chr1_1593… CRP 1.80e-5 CRP #> 10 rs6656924 159372915 RS6656924 chr1_1593… CRP 1.00e-6 CRP #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes "},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Calculate eQTLs service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"calculate_expression_quantitative_trait_loci( tissueSiteDetailId, gencodeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Notes output: Beta standard error recorded columns nes error respectively (see GTEx FAQs) variantId contains (order) chromosome, position, reference allele, alternative allele human genome build separated underscores. reference alternative alleles \"chr1_13550_G_A_b38\" example \"G\" \"\" respectively. See examples calculate minor alternative allele frequencies. Notes input: Argument variantId also accepts RSIDs.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\", gencodeId = \"ENSG00000203782.5\", variantId = \"rs79641866\") #> # A tibble: 1 × 15 #> data error gencodeId geneSymbol genotypes hetCount homoAltCount #> #> 1 0.148 ENSG00000… LOR 38 0 #> # ℹ 8 more variables: homoRefCount , maf , nes , pValue , #> # pValueThreshold , tStatistic , tissueSiteDetailId , #> # variantId # unnest list columns with tidyr::unnest() calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\", gencodeId = \"ENSG00000203782.5\", variantId = \"rs79641866\") |> tidyr::unnest(c(\"data\", \"genotypes\")) #> # A tibble: 670 × 15 #> data error gencodeId geneSymbol genotypes hetCount homoAltCount #> #> 1 -0.175 0.148 ENSG00000203782.5 LOR 0 38 0 #> 2 -0.247 0.148 ENSG00000203782.5 LOR 0 38 0 #> 3 -1.27 0.148 ENSG00000203782.5 LOR 0 38 0 #> 4 -1.53 0.148 ENSG00000203782.5 LOR 0 38 0 #> 5 0.263 0.148 ENSG00000203782.5 LOR 0 38 0 #> 6 0.0467 0.148 ENSG00000203782.5 LOR 0 38 0 #> 7 -1.42 0.148 ENSG00000203782.5 LOR 0 38 0 #> 8 -1.88 0.148 ENSG00000203782.5 LOR 0 38 0 #> 9 1.42 0.148 ENSG00000203782.5 LOR 0 38 0 #> 10 1.98 0.148 ENSG00000203782.5 LOR 0 38 0 #> # ℹ 660 more rows #> # ℹ 8 more variables: homoRefCount , maf , nes , pValue , #> # pValueThreshold , tStatistic , tissueSiteDetailId , #> # variantId # to calculate minor and alternative allele frequencies calculate_expression_quantitative_trait_loci( tissueSiteDetailId = \"Liver\", gencodeId = \"ENSG00000237973.1\", variantId = \"rs12119111\" ) |> dplyr::bind_rows(.id = \"rsid\") |> tidyr::separate( col = \"variantId\", into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\" ) |> # ...then ascertain alternative_allele frequency dplyr::mutate( alt_allele_count = (2 * homoAltCount) + hetCount, total_allele_count = 2 * (homoAltCount + hetCount + homoRefCount), alternative_allele_frequency = alt_allele_count / total_allele_count ) |> dplyr::select( rsid, beta = nes, se = error, pValue, minor_allele_frequency = maf, alternative_allele_frequency, chromosome:genome_build, tissueSiteDetailId ) #> # A tibble: 1 × 12 #> rsid beta se pValue minor_allele_frequency alternative_allele_frequency #> #> 1 1 0.0270 0.0670 0.688 0.365 0.635 #> # ℹ 6 more variables: chromosome , position , reference_allele , #> # alternative_allele , genome_build , tissueSiteDetailId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Ieqtls — calculate_ieqtls","title":"Calculate Ieqtls — calculate_ieqtls","text":"Calculate Cell Specific eQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"calculate_ieqtls( cellType, tissueSiteDetailId, gencodeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Ieqtls — calculate_ieqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Ieqtls — calculate_ieqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"# \\dontrun{ # perform request calculate_ieqtls(cellType = \"Adipocytes\", tissueSiteDetailId = \"Adipose_Subcutaneous\", gencodeId = \"ENSG00000203782.5\", variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #> cellType data datasetId enrichmentScores gencodeId genotypes regressionCoord #> #> 1 Adipocyt… gtex_v8 ENSG0000… #> # ℹ 2 more variables: tissueSiteDetailId , variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Isqtls — calculate_isqtls","title":"Calculate Isqtls — calculate_isqtls","text":"Calculate Cell Specific sQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"calculate_isqtls( cellType, tissueSiteDetailId, phenotypeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Isqtls — calculate_isqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Isqtls — calculate_isqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"# \\dontrun{ # perform request calculate_isqtls(cellType = \"Neutrophils\", tissueSiteDetailId = \"Whole_Blood\", phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\", variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #> cellType data datasetId enrichmentScores phenotypeId tissueSiteDetailId #> #> 1 Neutrophils gtex_v8 chr1:15947:1… Whole_Blood #> # ℹ 3 more variables: variantId , genotypes , regressionCoord # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"calculate_splicing_quantitative_trait_loci( tissueSiteDetailId, phenotypeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_splicing_quantitative_trait_loci( tissueSiteDetailId = \"Whole_Blood\", phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\", variantId = \"chr1_14677_G_A_b38\") #> # A tibble: 1 × 14 #> data error genotypes hetCount homoAltCount homoRefCount maf nes #> #> 1 0.139 69 0 601 0.0515 0.757 #> # ℹ 6 more variables: pValue , pValueThreshold , phenotypeId , #> # tStatistic , tissueSiteDetailId , variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download — download","title":"Download — download","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download — download","text":"","code":"download( materialTypes = NULL, tissueSiteDetailIds = NULL, pathCategory = NULL, tissueSampleIds = NULL, sex = NULL, sortBy = NULL, sortDirection = NULL, searchTerm = NULL, sampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download — download","text":"materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download — download","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download — download","text":"Note: running request filters (.e. download()) raises error.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download — download","text":"","code":"# \\dontrun{ download( materialTypes = \"RNA:Total RNA\", tissueSiteDetailIds = \"Thyroid\", pathCategory = \"clean_specimens\", sex = \"male\", ageBrackets = \"50-59\" ) #> # A tibble: 1 × 26 #> materialType sampleId sampleIdUpper sex rin hasGTExImage concentration #> #> 1 RNA:Total RNA GTEX-WYJK-… GTEX-WYJK-16… male 7.28 TRUE 36.4 #> # ℹ 19 more variables: analysisRelease , genotype , hardyScale , #> # pathologyNotes , subjectId , tissueSiteDetailId , #> # hasGenotype , originalMaterialType , aliquotId , #> # tissueSampleId , ageBracket , brainTissueDonor , #> # volume , hasExpressionData , hasBRDImage , #> # tissueSiteDetail , pathologyNotesCategories , #> # amount , tissueSite # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotation — get_annotation","title":"Get Annotation — get_annotation","text":"service returns list annotations allowed values particular dataset can subsetted. Results may filtered dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotation — get_annotation","text":"","code":"get_annotation(datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotation — get_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotation — get_annotation","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Annotation — get_annotation","text":"Note: output function appears incomplete currently.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotation — get_annotation","text":"","code":"# \\dontrun{ get_annotation() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 5 #> entity values type annotation datasetId #> #> 1 subject enum sex gtex_v8 #> 2 subject enum ageBracket gtex_v8 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"Find median transcript expression data along hierarchical clusters. Returns median normalized transcript expression tissues known transcripts given gene along hierarchical clustering results tissues transcripts, based exon expression, Newick format. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"get_clustered_median_exon_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"# \\dontrun{ get_clustered_median_exon_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 216 × 8 #> median exonId tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #> #> 1 0.789 ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… CRP #> 2 16.8 ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… CRP #> 3 0.0921 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… CRP #> 4 12 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… CRP #> 5 1 ENSG000… Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP #> 6 22.7 ENSG000… Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP #> 7 0 ENSG000… Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP #> 8 8 ENSG000… Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP #> 9 0 ENSG000… Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP #> 10 14 ENSG000… Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP #> # ℹ 206 more rows #> # ℹ 1 more variable: unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_exon_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $exon #> [1] \"((ENSG00000203782.5_2:8.51,ENSG00000132693.12_2:8.51):0.79,(ENSG00000203782.5_1:5.92,ENSG00000132693.12_1:5.92):3.38);\" #> #> $tissue #> [1] \"(((((((((((Uterus:0.02,Stomach:0.02):0.04,(Pituitary:0.02,Brain_Cerebellum:0.02):0.04):0.01,((((Thyroid:0.03,Colon_Transverse:0.03):0.00,((Artery_Coronary:0.02,Adipose_Visceral_Omentum:0.02):0.00,(Esophagus_Muscularis:0.01,Esophagus_Gastroesophageal_Junction:0.01):0.01):0.01):0.01,Small_Intestine_Terminal_Ileum:0.04):0.00,Artery_Aorta:0.04):0.03):0.04,Kidney_Cortex:0.11):0.00,Brain_Cerebellar_Hemisphere:0.11):0.02,(((((((Ovary:0.01,Nerve_Tibial:0.01):0.00,Adipose_Subcutaneous:0.01):0.01,Esophagus_Mucosa:0.02):0.01,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.02):0.01,Minor_Salivary_Gland:0.03):0.01,(Prostate:0.02,Lung:0.02):0.02):0.04,Testis:0.09):0.04):0.02,((Fallopian_Tube:0.09,Cervix_Ectocervix:0.09):0.01,((Kidney_Medulla:0.06,Bladder:0.06):0.03,((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.04,Cervix_Endocervix:0.05):0.03):0.02):0.05):0.03,((Vagina:0.09,Brain_Hypothalamus:0.09):0.03,((((((Brain_Hippocampus:0.01,Brain_Amygdala:0.01):0.01,Cells_EBV-transformed_lymphocytes:0.02):0.01,Brain_Frontal_Cortex_BA9:0.02):0.01,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.03):0.02,(Brain_Cortex:0.02,Brain_Anterior_cingulate_cortex_BA24:0.02):0.03):0.02,(((((Brain_Substantia_nigra:0.01,Artery_Tibial:0.01):0.00,(Heart_Atrial_Appendage:0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00):0.00,Muscle_Skeletal:0.01):0.01,Colon_Sigmoid:0.02):0.01,(Whole_Blood:0.02,Heart_Left_Ventricle:0.02):0.02):0.04):0.05):0.06):0.20,Pancreas:0.39):0.34,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.71):0.12,Liver:0.85);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues along hierarchical clustering results tissues genes, based gene expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"get_clustered_median_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"# \\dontrun{ get_clustered_median_gene_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 108 × 7 #> median tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 0.347 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 0.240 Adipose_Visceral_Omen… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 0.384 Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 0.198 Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 0.332 Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 0.117 Artery_Tibial UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 7 0.631 Bladder UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 8 0.0347 Brain_Amygdala UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 98 more rows # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_gene_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $gene #> [1] \"Not enough data. At least three data sets are required for clustering.\" #> #> $tissue #> [1] \"(((((((((((Cells_Cultured_fibroblasts:0.01,Bladder:0.01):0.01,Prostate:0.02):0.01,(Testis:0.02,Lung:0.02):0.02):0.01,(((((Thyroid:0.01,Minor_Salivary_Gland:0.01):0.01,Uterus:0.01):0.00,(((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.01,Small_Intestine_Terminal_Ileum:0.01):0.00,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.01):0.01):0.00,((Esophagus_Gastroesophageal_Junction:0.00,Adipose_Visceral_Omentum:0.00):0.00,Esophagus_Muscularis:0.01):0.01):0.01,((Ovary:0.00,Nerve_Tibial:0.00):0.01,Esophagus_Mucosa:0.01):0.02):0.01):0.00,(((((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.00,Colon_Transverse:0.01):0.01,Adrenal_Gland:0.02):0.00,(Kidney_Medulla:0.01,Kidney_Cortex:0.01):0.01):0.02):0.01,((((Whole_Blood:0.01,Heart_Left_Ventricle:0.01):0.01,Brain_Cerebellar_Hemisphere:0.02):0.01,(((Colon_Sigmoid:0.01,Brain_Substantia_nigra:0.01):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.01):0.01):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Amygdala:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.01):0.00,Brain_Anterior_cingulate_cortex_BA24:0.01):0.00,Brain_Hippocampus:0.01):0.01,(Artery_Tibial:0.01,Artery_Aorta:0.01):0.01):0.01):0.02):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Brain_Frontal_Cortex_BA9:0.02):0.03,Vagina:0.05):0.02):0.03,((Cervix_Endocervix:0.02,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.04):0.07):0.10,Pancreas:0.20):0.37,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.07,Liver:0.64);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"Find median junction expression data along hierarchical clusters. Returns median junction read counts tissues given gene known transcripts along hierarchical clustering results tissues genes, based junction expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"get_clustered_median_junction_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"# \\dontrun{ get_clustered_median_junction_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 432 × 8 #> median junctionId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 2 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 3 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 4 0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 5 0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 6 0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 7 0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 8 0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 9 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 10 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol , unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_junction_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $junction #> [1] \"((((((chr1_159713641_159714006:0.03,chr1_159713604_159714002:0.03):0.67,(chr1_159712795_159714006:0.01,chr1_159712581_159713502:0.01):0.69):0.56,chr1_159712795_159713502:1.26):0.90,chr1_159713973_159714498:2.16):0.54,chr1_159714139_159714424:2.70):2.61,chr1_153259734_153260926:5.31);\" #> #> $tissue #> [1] \"(((((((((((((((((Adipose_Visceral_Omentum:0.00,Adipose_Subcutaneous:0.00):0.00,Artery_Aorta:0.00):0.00,Artery_Coronary:0.00):0.00,Artery_Tibial:0.00):0.00,Brain_Cortex:0.00):0.00,Breast_Mammary_Tissue:0.00):0.00,Colon_Sigmoid:0.00):0.00,Heart_Atrial_Appendage:0.00):0.00,Muscle_Skeletal:0.00):0.00,Nerve_Tibial:0.00):0.00,Vagina:0.00):0.08,Kidney_Medulla:0.08):0.03,(((((((((((((((((((((Brain_Amygdala:0.00,Bladder:0.00):0.00,Brain_Anterior_cingulate_cortex_BA24:0.00):0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Cerebellar_Hemisphere:0.00):0.00,Brain_Cerebellum:0.00):0.00,Brain_Frontal_Cortex_BA9:0.00):0.00,Brain_Hippocampus:0.00):0.00,Brain_Hypothalamus:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Brain_Substantia_nigra:0.00):0.00,Cells_EBV-transformed_lymphocytes:0.00):0.00,Colon_Transverse:0.00):0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Esophagus_Muscularis:0.00):0.00,Heart_Left_Ventricle:0.00):0.00,Kidney_Cortex:0.00):0.00,Pituitary:0.00):0.00,Thyroid:0.00):0.00,Whole_Blood:0.00):0.11):0.03,((((((((((((Cells_Cultured_fibroblasts:0.00,Adrenal_Gland:0.00):0.00,Esophagus_Mucosa:0.00):0.00,Fallopian_Tube:0.00):0.00,Lung:0.00):0.00,Minor_Salivary_Gland:0.00):0.00,Ovary:0.00):0.00,Prostate:0.00):0.00,Small_Intestine_Terminal_Ileum:0.00):0.00,Spleen:0.00):0.00,Stomach:0.00):0.00,Uterus:0.00):0.06,((Cervix_Endocervix:0.00,Cervix_Ectocervix:0.00):0.00,Testis:0.00):0.06):0.09):0.19,Pancreas:0.33):0.27,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.59):0.68,Liver:1.29);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"Find median transcript expression data known transcripts gene along hierarchical clusters. Returns median normalized expression tissues known transcripts given gene along hierarchical clustering results tissues genes, based expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"get_clustered_median_transcript_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"# \\dontrun{ get_clustered_median_transcript_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 432 × 8 #> median transcriptId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0.130 ENST00000255030.9 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 2 0 ENST00000368110.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 3 0 ENST00000368111.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 4 0 ENST00000368112.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 5 0 ENST00000437342.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 6 0.0100 ENST00000473196.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 7 0 ENST00000489317.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 9 0 ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 10 0 ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol , unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_transcript_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $transcript #> [1] \"(((ENST00000473196.1:0.46,ENST00000255030.9:0.46):1.64,(((ENST00000437342.1:0.16,ENST00000368112.5:0.16):0.09,(ENST00000368111.5:0.03,ENST00000368110.1:0.03):0.21):0.15,ENST00000489317.1:0.40):1.70):2.76,ENST00000368742.3:4.86);\" #> #> $tissue #> [1] \"(((((((((((Spleen:0.00,Breast_Mammary_Tissue:0.00):0.01,Lung:0.01):0.00,((Ovary:0.01,Esophagus_Mucosa:0.01):0.00,Nerve_Tibial:0.01):0.01):0.00,((((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.00,Adipose_Visceral_Omentum:0.01):0.00,((Esophagus_Muscularis:0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Thyroid:0.00):0.00):0.00,(Small_Intestine_Terminal_Ileum:0.01,Artery_Aorta:0.01):0.01):0.00):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Hippocampus:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Artery_Tibial:0.01):0.00,Brain_Amygdala:0.01):0.01,(((Brain_Putamen_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,((Colon_Sigmoid:0.00,Brain_Substantia_nigra:0.00):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00):0.01):0.01):0.01,((((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.01,Kidney_Cortex:0.01):0.00,((Uterus:0.01,Prostate:0.01):0.00,Minor_Salivary_Gland:0.01):0.01):0.00,((((Heart_Left_Ventricle:0.01,Colon_Transverse:0.01):0.00,(Whole_Blood:0.00,Brain_Cerebellar_Hemisphere:0.00):0.01):0.00,((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.01):0.00,Kidney_Medulla:0.02):0.01):0.01):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Vagina:0.02):0.01,(Brain_Frontal_Cortex_BA9:0.01,Brain_Anterior_cingulate_cortex_BA24:0.01):0.02):0.03):0.01,((((Cervix_Endocervix:0.02,Bladder:0.02):0.00,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.03):0.02,Testis:0.05):0.01):0.15,Pancreas:0.21):0.36,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.61,Liver:1.19);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"service returns collapsed exons gene model given gene. Gene-level exon-level expression quantification based GENCODE annotation, collapsed single transcript model gene using algorithm developed GTEx analysis team. default, service queries models used latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"get_collapsed_gene_model_exon( gencodeId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{ get_collapsed_gene_model_exon(gencodeId = \"ENSG00000132693.12\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> featureType end genomeBuild chromosome exonNumber geneSymbolUpper exonId #> #> 1 exon 159714589 GRCh38/hg38 chr1 1 CRP ENSG0… #> 2 exon 159714138 GRCh38/hg38 chr1 2 CRP ENSG0… #> # ℹ 7 more variables: datasetId , start , dataSource , #> # gencodeId , geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Dataset Info — get_dataset_info","title":"Get Dataset Info — get_dataset_info","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Dataset Info — get_dataset_info","text":"","code":"get_dataset_info(datasetId = \"gtex_v8\", organizationName = \"GTEx Consortium\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Dataset Info — get_dataset_info","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Dataset Info — get_dataset_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Dataset Info — get_dataset_info","text":"Note: current returns empty values.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Dataset Info — get_dataset_info","text":"","code":"# \\dontrun{ get_dataset_info() #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Downloads Page Data — get_downloads_page_data","title":"Get Downloads Page Data — get_downloads_page_data","text":"Retrieves files belonging given project_id display Downloads Page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"get_downloads_page_data(project_id = \"adult-gtex\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Downloads Page Data — get_downloads_page_data","text":"project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Downloads Page Data — get_downloads_page_data","text":"Tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Downloads Page Data — get_downloads_page_data","text":"Note: GTEx Portal API documentation states \"GTEx currently one project available: gtex\". However, project_id values \"adult-gtex\" \"egtex\" return results, whereas \"gtex\" (see examples).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"# \\dontrun{ # \"adult-gtex\" (default `project_id` value) and \"egtex\" both return results get_downloads_page_data() #> # A tibble: 9 × 6 #> name displayName description order parent children #> #> 1 gs://adult-gtex/bulk-gex/ Bulk tissu… \"\" 1 gs://… #> 2 gs://adult-gtex/bulk-qtl/ QTL \"\" 2 gs://… #> 3 gs://adult-gtex/single-cell/ Single cell \"\" 3 gs://… #> 4 gs://adult-gtex/long-read-d… Long read … \"Long Read… 4 gs://… #> 5 gs://adult-gtex/haplotype-e… Haplotype … \"Haplotype… 5 gs://… #> 6 gs://adult-gtex/variants/ Variants \"\" 6 gs://… #> 7 gs://adult-gtex/references/ Reference \"\" 7 gs://… #> 8 gs://adult-gtex/annotations/ Metadata \"\" 8 gs://… #> 9 gs://adult-gtex/additional_… Additional… \"\" 9 gs://… egtex <- get_downloads_page_data(\"egtex\") egtex #> # A tibble: 3 × 6 #> name displayName description order parent children #> #> 1 gs://egtex/methylation/ Methylation \"\" 1 gs://… #> 2 gs://egtex/proteomics/ Proteomics \"Protein and RN… 2 gs://… #> 3 gs://egtex/telomeres/ Telomeres \"Relative telom… 3 gs://… # ...\"gtex\" does not get_downloads_page_data(\"gtex\") #> # A tibble: 0 × 0 # get details for whole blood methylation data, including download URL purrr::pluck( egtex$children, 1, \"folders\", \"Methylation - EPIC Array\", \"children\", \"folders\", \"mQTLs\", \"children\", \"files\", \"WholeBlood.mQTLs.regular.txt.gz\" ) #> $displayName #> [1] \"WholeBlood.mQTLs.regular.txt.gz\" #> #> $description #> [1] \"\" #> #> $fileSize #> [1] 43461408219 #> #> $url #> [1] \"https://storage.googleapis.com/egtex/methylation/epic-arrays/mQTLs/WholeBlood.mQTLs.regular.txt.gz\" #> #> $order #> [1] 27 #> #> $parent #> [1] \"gs://egtex/methylation/epic-arrays/mQTLs/\" #> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Eqtl Genes — get_eqtl_genes","title":"Get Eqtl Genes — get_eqtl_genes","text":"Retrieve eGenes (eQTL Genes). service returns eGenes (eQTL Genes) specified dataset. eGenes genes least one significant cis-eQTL acting upon . Results may filtered tissue. default, service queries latest GTEx release. eGene, results include allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), q-value (qValue). log2AllelicFoldChange allelic fold change (log2 scale) significant eQTL. pValue nominal p-value significant eQTL. pValueThreshold p-value threshold used determine whether cis-eQTL gene significant. details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods. empiricalPValue beta distribution-adjusted empirical p-value FastQTL. qValues calculated based empirical p-values. false discovery rate (FDR) threshold <= 0.05 applied identify genes significant eQTL. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"get_eqtl_genes( tissueSiteDetailIds, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Eqtl Genes — get_eqtl_genes","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Eqtl Genes — get_eqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"# \\dontrun{ get_eqtl_genes(c(\"Whole_Blood\", \"Artery_Aorta\")) #> Warning: ! Total number of items (24853) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 100 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 24853 #> # A tibble: 250 × 10 #> tissueSiteDetailId ontologyId datasetId empiricalPValue gencodeId geneSymbol #> #> 1 Whole_Blood UBERON:001… gtex_v8 1.05e- 9 ENSG0000… WASH7P #> 2 Whole_Blood UBERON:001… gtex_v8 1.06e-25 ENSG0000… RP11-34P1… #> 3 Whole_Blood UBERON:001… gtex_v8 6.31e- 2 ENSG0000… CICP27 #> 4 Whole_Blood UBERON:001… gtex_v8 8.71e- 9 ENSG0000… RP11-34P1… #> 5 Whole_Blood UBERON:001… gtex_v8 6.01e-20 ENSG0000… RP11-34P1… #> 6 Whole_Blood UBERON:001… gtex_v8 6.96e- 9 ENSG0000… RP11-34P1… #> 7 Whole_Blood UBERON:001… gtex_v8 3.10e- 4 ENSG0000… RP11-34P1… #> 8 Whole_Blood UBERON:001… gtex_v8 1.92e- 3 ENSG0000… ABC7-4304… #> 9 Whole_Blood UBERON:001… gtex_v8 1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood UBERON:001… gtex_v8 7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange , pValue , #> # pValueThreshold , qValue # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Exons — get_exons","title":"Get Exons — get_exons","text":"service returns exons known transcripts given gene. versioned GENCODE ID required ensure exons single gene. dataset ID GENCODE version genome build must provided. Although annotated exons dataset dependent, specifying dataset equivalent specifying GENCODE version genome build used dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Exons — get_exons","text":"","code":"get_exons( gencodeId, gencodeVersion = NULL, genomeBuild = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Exons — get_exons","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Exons — get_exons","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Exons — get_exons","text":"","code":"# \\dontrun{ get_exons(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #> featureType end genomeBuild start exonId source chromosome gencodeId #> #> 1 exon 153259733 GRCh38/hg38 153259700 ENSE0… HAVANA chr1 ENSG0000… #> 2 exon 153262122 GRCh38/hg38 153260927 ENSE0… HAVANA chr1 ENSG0000… #> # ℹ 5 more variables: transcriptId , geneSymbol , #> # gencodeVersion , strand , exonNumber # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Expression Pca — get_expression_pca","title":"Get Expression Pca — get_expression_pca","text":"Find gene expression PCA data. Returns gene expression PCA (principal component analysis) tissues. Results may filtered tissue, sample, dataset. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Expression Pca — get_expression_pca","text":"","code":"get_expression_pca( tissueSiteDetailIds, datasetId = \"gtex_v8\", sampleId = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Expression Pca — get_expression_pca","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Expression Pca — get_expression_pca","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Expression Pca — get_expression_pca","text":"","code":"# \\dontrun{ get_expression_pca(tissueSiteDetailIds = c(\"Adipose_Subcutaneous\", \"Whole_Blood\")) #> Warning: ! Total number of items (1418) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1418 #> # A tibble: 250 × 7 #> pc1 pc2 pc3 sampleId tissueSiteDetailId ontologyId datasetId #> #> 1 0.0385 -0.0178 0.0769 GTEX-1117F… Adipose_Subcutane… UBERON:00… gtex_v8 #> 2 -0.0585 0.00809 0.00492 GTEX-111CU… Adipose_Subcutane… UBERON:00… gtex_v8 #> 3 0.140 -0.0308 -0.0368 GTEX-111FC… Adipose_Subcutane… UBERON:00… gtex_v8 #> 4 0.0597 0.140 0.0294 GTEX-111VG… Adipose_Subcutane… UBERON:00… gtex_v8 #> 5 -0.0968 0.00233 -0.0174 GTEX-111YS… Adipose_Subcutane… UBERON:00… gtex_v8 #> 6 -0.120 0.0195 -0.0594 GTEX-1122O… Adipose_Subcutane… UBERON:00… gtex_v8 #> 7 -0.102 0.0652 0.00344 GTEX-1128S… Adipose_Subcutane… UBERON:00… gtex_v8 #> 8 0.105 0.0174 -0.0568 GTEX-113IC… Adipose_Subcutane… UBERON:00… gtex_v8 #> 9 -0.109 -0.0543 0.00594 GTEX-117YX… Adipose_Subcutane… UBERON:00… gtex_v8 #> 10 0.132 -0.0335 -0.0350 GTEX-11DXW… Adipose_Subcutane… UBERON:00… gtex_v8 #> # ℹ 240 more rows get_expression_pca(tissueSiteDetailIds = \"Adipose_Subcutaneous\", sampleId = \"GTEX-1117F-0226-SM-5GZZ7\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #> pc1 pc2 pc3 sampleId tissueSiteDetailId ontologyId datasetId #> #> 1 0.0385 -0.0178 0.0769 GTEX-1117F-0226… Adipose_Subcutane… UBERON:00… gtex_v8 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Get File List — get_file_list","title":"Get File List — get_file_list","text":"Get files GTEx dataset Download page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get File List — get_file_list","text":"","code":"get_file_list()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get File List — get_file_list","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get File List — get_file_list","text":"returned tibble includes nested list column, \"filesets\". details files, sub-categorised fileset (see examples section).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get File List — get_file_list","text":"","code":"# \\dontrun{ # Column \"filesets\" is a list column get_file_list() #> # A tibble: 11 × 10 #> name subpath dbgapId dataset release order type id description #> #> 1 GTEx Analysis … gtex_a… \"phs00… GTEx v3 10 data… gtex… \"\" #> 2 GTEx Analysis … gtex_a… \"\" GTEx v6p 7 data… gtex… \"The GTEx … #> 3 Biobank Invent… gtex_b… \"\" GTEx biobank 5 data… biob… \"\" #> 4 GTEx Analysis … gtex_a… \"phs00… GTEx v7 6 data… gtex… \"\" #> 5 GTEx Analysis … gtex_a… \"phs00… GTEx v6 8 data… gtex… \"\" #> 6 Additional Dat… gtex_a… \"\" GTEx additi… 3 data… addi… \"\" #> 7 GTEx Analysis … gtex_a… \"phs00… GTEx v4 9 data… gtex… \"\" #> 8 External Datas… gtex_e… \"\" GTEx extern… 4 data… exte… \"\" #> 9 GTEx Analysis … gtex_a… \"phs00… GTEx v8 1 data… gtex… \"The GTEx … #> 10 eGTEx gtex_e… \"\" GTEx egtex 2 data… egtex \"The Enhan… #> 11 GTEx Analysis … gtex_a… \"phs00… GTEx v9 0 data… gtex… \"Open-acce… #> # ℹ 1 more variable: filesets # Get \"GTEx Analysis V9\" file list gtex_v9_files <- get_file_list() |> dplyr::filter(name == \"GTEx Analysis V9\") |> dplyr::pull(filesets) # \"GTEx Analysis V9\" filesets names(gtex_v9_files[[1]]) #> [1] \"snRNA-Seq Data\" \"Long Read Data\" # \"GTEx Analysis V9\", \"snRNA-Seq Data\" fileset files names(gtex_v9_files[[1]][[\"snRNA-Seq Data\"]]$files) #> [1] \"GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad\" #> [2] \"GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad\" # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Fine Mapping — get_fine_mapping","title":"Get Fine Mapping — get_fine_mapping","text":"Retrieve Fine Mapping Data Finds returns Fine Mapping data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"get_fine_mapping( gencodeIds, datasetId = \"gtex_v8\", variantId = NULL, tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Fine Mapping — get_fine_mapping","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". variantId String. gtex variant ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Fine Mapping — get_fine_mapping","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"# \\dontrun{ # search by gene get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 27 #> # A tibble: 27 × 9 #> datasetId gencodeId method pip setId setSize tissueSiteDetailId #> #> 1 gtex_v8 ENSG00000132693.12 DAP-G 0.0235 1 5 Thyroid #> 2 gtex_v8 ENSG00000132693.12 DAP-G 0.0221 1 5 Thyroid #> 3 gtex_v8 ENSG00000132693.12 DAP-G 0.0171 1 5 Thyroid #> 4 gtex_v8 ENSG00000132693.12 DAP-G 0.0252 1 5 Thyroid #> 5 gtex_v8 ENSG00000132693.12 DAP-G 0.892 1 5 Thyroid #> 6 gtex_v8 ENSG00000203782.5 DAP-G 0.0126 1 22 Whole_Blood #> 7 gtex_v8 ENSG00000203782.5 DAP-G 0.00690 1 22 Whole_Blood #> 8 gtex_v8 ENSG00000203782.5 DAP-G 0.0313 1 22 Whole_Blood #> 9 gtex_v8 ENSG00000203782.5 DAP-G 0.00852 1 22 Whole_Blood #> 10 gtex_v8 ENSG00000203782.5 DAP-G 0.0105 1 22 Whole_Blood #> # ℹ 17 more rows #> # ℹ 2 more variables: ontologyId , variantId # optionally filter for a single variant and/or one or more tissues get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), variantId = \"chr1_153228363_A_G_b38\", tissueSiteDetailIds = c(\"Whole_Blood\", \"Thyroid\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 9 #> datasetId gencodeId method pip setId setSize tissueSiteDetailId ontologyId #> #> 1 gtex_v8 ENSG00000… DAP-G 0.0126 1 22 Whole_Blood UBERON:00… #> # ℹ 1 more variable: variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"service allows user query full Collapsed Gene Model Exon specific gene gencode ID GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"get_full_get_collapsed_gene_model_exon(gencodeId, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{ get_full_get_collapsed_gene_model_exon(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> featureType end genomeBuild chromosome exonNumber geneSymbolUpper exonId #> #> 1 exon 153259733 GRCh38/hg38 chr1 1 LOR ENSG0… #> 2 exon 153262122 GRCh38/hg38 chr1 2 LOR ENSG0… #> # ℹ 7 more variables: datasetId , start , dataSource , #> # gencodeId , geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Functional Annotation — get_functional_annotation","title":"Get Functional Annotation — get_functional_annotation","text":"endpoint retrieves functional annotation certain chromosome location. Default recent dataset release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"get_functional_annotation( datasetId = \"gtex_v8\", chromosome, start, end, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Functional Annotation — get_functional_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". start Integer. end Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Functional Annotation — get_functional_annotation","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"# \\dontrun{ get_functional_annotation(chromosome = \"chr1\", start = 192168000, end = 192169000) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3 #> # A tibble: 3 × 23 #> variantId enhancer promoter openChromatinRegion promoterFlankingRegion #> #> 1 chr1_192168015_T… TRUE FALSE FALSE FALSE #> 2 chr1_192168266_T… TRUE FALSE FALSE FALSE #> 3 chr1_192168728_T… FALSE FALSE FALSE FALSE #> # ℹ 18 more variables: ctcfBindingSite , tfBindingSite , #> # `3PrimeUtrVariant` , `5PrimeUtrVariant` , #> # frameshiftVariant , intronVariant , missenseVariant , #> # nonCodingTranscriptExonVariant , spliceAcceptorVariant , #> # spliceDonorVariant , spliceRegionVariant , stopGained , #> # synonymousVariant , chromosome , pos , ref , alt , #> # datasetId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Expression — get_gene_expression","title":"Get Gene Expression — get_gene_expression","text":"Find normalized gene expression data. Returns normalized gene expression tissues sample level. Results may filtered dataset, gene tissue, least one gene must provided. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Expression — get_gene_expression","text":"","code":"get_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, attributeSubset = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Expression — get_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Expression — get_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Expression — get_gene_expression","text":"","code":"# \\dontrun{ # multiple genes, selected tissues get_gene_expression(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), tissueSiteDetailIds = c(\"Thyroid\", \"Whole_Blood\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Thyroid UBERON:00… gtex_v8 ENSG0000… LOR TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… LOR TPM #> 3 Thyroid UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # single gene, selected (single) tissue get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # subset by sex get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\", attributeSubset = \"sex\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 2 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # subset by age bracket get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\", attributeSubset = \"ageBracket\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 6 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Search — get_gene_search","title":"Get Gene Search — get_gene_search","text":"Find genes partial complete match gene_id gene_id gene symbol, gencode ID, Ensemble ID Gencode Version Genome Build must specified GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Search — get_gene_search","text":"","code":"get_gene_search( geneId, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Search — get_gene_search","text":"geneId String. gene symbol, gencode ID, Ensemble ID. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Search — get_gene_search","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Search — get_gene_search","text":"","code":"# \\dontrun{ get_gene_search(\"CRP\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #> chromosome dataSource description end gencodeId gencodeVersion geneStatus #> #> 1 chr1 HAVANA C-reactive p… 1.60e8 ENSG0000… v26 \"\" #> 2 chr1 HAVANA C-reactive p… 1.60e8 ENSG0000… v26 \"\" #> # ℹ 8 more variables: geneSymbol , geneSymbolUpper , geneType , #> # genomeBuild , start , strand , tss , entrezGeneId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genes — get_genes","title":"Get Genes — get_genes","text":"service returns information reference genes. genome build GENCODE version must provided. Genes searchable gene symbol, GENCODE ID versioned GENCODE ID. Versioned GENCODE ID recommended ensure unique ID matching. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genes — get_genes","text":"","code":"get_genes( geneIds, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genes — get_genes","text":"geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genes — get_genes","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genes — get_genes","text":"","code":"# \\dontrun{ get_genes(c(\"CRP\", \"IL6R\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #> chromosome dataSource description end entrezGeneId gencodeId gencodeVersion #> #> 1 chr1 HAVANA interleuki… 1.54e8 3570 ENSG0000… v26 #> 2 chr1 HAVANA C-reactive… 1.60e8 1401 ENSG0000… v26 #> # ℹ 8 more variables: geneStatus , geneSymbol , #> # geneSymbolUpper , geneType , genomeBuild , start , #> # strand , tss # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genomic Features — get_genomic_features","title":"Get Genomic Features — get_genomic_features","text":"GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genomic Features — get_genomic_features","text":"","code":"get_genomic_features(.featureId, datasetId = \"gtex_v8\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genomic Features — get_genomic_features","text":".featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genomic Features — get_genomic_features","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Genomic Features — get_genomic_features","text":"endpoint takes path parameter \"featureId\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genomic Features — get_genomic_features","text":"","code":"# \\dontrun{ # gene symbol get_genomic_features(\"brca1\") #> # A tibble: 1 × 17 #> gencodeVersion end description geneSymbolUpper genomeBuild geneStatus #> #> 1 v26 43170245 BRCA1, DNA rep… BRCA1 GRCh38/hg38 \"\" #> # ℹ 11 more variables: strand , entrezGeneId , geneType , #> # start , dataSource , gencodeId , geneSymbol , #> # tss , chromosome , featureType , assembly # GENCODE ID get_genomic_features(\"ENSG00000132693.12\") #> # A tibble: 1 × 17 #> gencodeVersion end description geneSymbolUpper genomeBuild geneStatus #> #> 1 v26 159714589 C-reactive pr… CRP GRCh38/hg38 \"\" #> # ℹ 11 more variables: strand , entrezGeneId , geneType , #> # start , dataSource , gencodeId , geneSymbol , #> # tss , chromosome , featureType , assembly # RSID get_genomic_features(\"rs1815739\") #> # A tibble: 1 × 8 #> featureType chromosome start snpId variantId ref alt assembly #> #> 1 snp chr11 66560624 rs1815739 chr11_66560624… C T HG38 # GTEx variant ID get_genomic_features(\"chr11_66561023_G_GTTA_b38\") #> # A tibble: 1 × 8 #> featureType chromosome start snpId variantId ref alt assembly #> #> 1 snp chr11 66561023 rs3837428 chr11_66561023… G GTTA HG38 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"Find GWAS Catalog certain chromosome start end locations. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"get_gwas_catalog_by_location( start, end, chromosome, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"# \\dontrun{ get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = \"chr1\") #> Warning: ! Total number of items (316) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 316 #> # A tibble: 250 × 10 #> chromosome start end phenotype pValue beta pubmedId snpId riskAllele #> #> 1 chr1 9653328 9653329 Testicula… 6e-13 1.14 28604728 rs42… T #> 2 chr1 8428505 8428506 Autism sp… 7e- 9 1.06 28540026 rs30… ? #> 3 chr1 9651584 9651585 Monocyte … 2e- 9 0.0222 27863252 rs75… G #> 4 chr1 3080038 3080039 Mean corp… 1e-13 0.0311 27863252 rs15… C #> 5 chr1 3811497 3811498 Mean corp… 1e-13 0.0301 27863252 rs12… T #> 6 chr1 4544044 4544045 Adolescen… 3e- 9 1.2 26394188 rs24… ? #> 7 chr1 1312114 1312115 Inflammat… 8e-13 1.10 23128233 rs12… A #> 8 chr1 7961913 7961914 Inflammat… 1e-15 1.11 23128233 rs35… G #> 9 chr1 8444361 8444362 Eosinophi… 2e-19 0.0328 27863252 rs15… A #> 10 chr1 9281727 9281728 Eosinophi… 1e-10 0.0260 27863252 rs67… T #> # ℹ 240 more rows #> # ℹ 1 more variable: genomeBuild # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Image — get_image","title":"Get Image — get_image","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Image — get_image","text":"","code":"get_image(tissueSampleIds = NULL, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Image — get_image","text":"tissueSampleIds Array strings. list Tissue Sample ID(s). page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Image — get_image","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Image — get_image","text":"","code":"# \\dontrun{ get_image() #> Warning: ! Total number of items (25713) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 103 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25713 #> # A tibble: 250 × 11 #> ageBracket hardyScale hide histologyImageId pathologyNotes sex subjectId #> #> 1 60-69 Slow death FALSE GTEX-1117F-0126 6 pieces, minim… fema… GTEX-111… #> 2 60-69 Slow death FALSE GTEX-1117F-0226 2 pieces, ~15% … fema… GTEX-111… #> 3 60-69 Slow death FALSE GTEX-1117F-0326 2 pieces, clean… fema… GTEX-111… #> 4 60-69 Slow death FALSE GTEX-1117F-0426 2 pieces, !5% f… fema… GTEX-111… #> 5 60-69 Slow death FALSE GTEX-1117F-0526 2 pieces, clean… fema… GTEX-111… #> 6 60-69 Slow death FALSE GTEX-1117F-0626 2 pieces, up to… fema… GTEX-111… #> 7 60-69 Slow death FALSE GTEX-1117F-0726 2 pieces, no ab… fema… GTEX-111… #> 8 60-69 Slow death FALSE GTEX-1117F-0826 2 pieces, exten… fema… GTEX-111… #> 9 60-69 Slow death FALSE GTEX-1117F-0926 6 pieces, adher… fema… GTEX-111… #> 10 60-69 Slow death FALSE GTEX-1117F-1026 2 pieces, moder… fema… GTEX-111… #> # ℹ 240 more rows #> # ℹ 4 more variables: tissueSiteDetail , sampleId , #> # tissueSampleId , pathologyNotesCategories # filter by `tissueSampleId` result <- get_image(tissueSampleIds = \"GTEX-1117F-0526\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 print(result) #> # A tibble: 1 × 11 #> ageBracket hardyScale hide histologyImageId pathologyNotes #> #> 1 60-69 Slow death FALSE GTEX-1117F-0526 2 pieces, clean, Monckebeg media… #> # ℹ 6 more variables: pathologyNotesCategories , sampleId , #> # sex , subjectId , tissueSampleId , tissueSiteDetail # note that `pathologyNotesCategories` (if present) is a list column print(result$pathologyNotesCategories) #> # A tibble: 1 × 2 #> monckeberg sclerotic #> #> 1 TRUE TRUE # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Independent Eqtl — get_independent_eqtl","title":"Get Independent Eqtl — get_independent_eqtl","text":"Retrieve Independent eQTL Data Finds returns Independent eQTL Data data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"get_independent_eqtl( gencodeIds, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Independent Eqtl — get_independent_eqtl","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Independent Eqtl — get_independent_eqtl","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"# \\dontrun{ # search by gene get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 8 #> # A tibble: 8 × 14 #> gencodeId geneSymbol variantId snpId tissueSiteDetailId ontologyId rank #> #> 1 ENSG0000013269… CRP chr1_160… rs66… Esophagus_Gastroe… UBERON:00… 1 #> 2 ENSG0000013269… CRP chr1_159… rs57… Thyroid UBERON:00… 1 #> 3 ENSG0000020378… LOR chr1_153… rs14… Artery_Coronary UBERON:00… 1 #> 4 ENSG0000020378… LOR chr1_153… rs87… Whole_Blood UBERON:00… 1 #> 5 ENSG0000020378… LOR chr1_153… rs12… Skin_Sun_Exposed_… UBERON:00… 1 #> 6 ENSG0000020378… LOR chr1_152… rs77… Heart_Atrial_Appe… UBERON:00… 1 #> 7 ENSG0000020378… LOR chr1_153… rs12… Esophagus_Mucosa UBERON:00… 1 #> 8 ENSG0000013269… CRP chr1_159… rs86… Muscle_Skeletal UBERON:00… 1 #> # ℹ 7 more variables: tssDistance , maf , pValue , nes , #> # chromosome , pos , datasetId # optionally filter for a single variant and/or one or more tissues get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), tissueSiteDetailIds = c(\"Whole_Blood\", \"Thyroid\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> gencodeId geneSymbol variantId snpId tissueSiteDetailId ontologyId rank #> #> 1 ENSG0000013269… CRP chr1_159… rs57… Thyroid UBERON:00… 1 #> 2 ENSG0000020378… LOR chr1_153… rs87… Whole_Blood UBERON:00… 1 #> # ℹ 7 more variables: tssDistance , maf , pValue , nes , #> # chromosome , pos , datasetId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"Find linkage disequilibrium (LD) data given variant GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data( variantId, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"variantId String. gtex variant ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(\"chr1_159245536_C_T_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 241 #> # A tibble: 241 × 3 #> variantId_1 variantId_2 ld #> #> 1 chr1_159163610_GA_G_b38 chr1_159245536_C_T_b38 0.114 #> 2 chr1_159163924_G_A_b38 chr1_159245536_C_T_b38 0.114 #> 3 chr1_159164864_T_C_b38 chr1_159245536_C_T_b38 0.114 #> 4 chr1_159165054_A_G_b38 chr1_159245536_C_T_b38 0.113 #> 5 chr1_159165563_T_C_b38 chr1_159245536_C_T_b38 0.113 #> 6 chr1_159174791_T_C_b38 chr1_159245536_C_T_b38 0.252 #> 7 chr1_159176518_G_T_b38 chr1_159245536_C_T_b38 0.146 #> 8 chr1_159176900_C_A_b38 chr1_159245536_C_T_b38 0.271 #> 9 chr1_159177147_A_T_b38 chr1_159245536_C_T_b38 0.274 #> 10 chr1_159179691_T_C_b38 chr1_159245536_C_T_b38 0.253 #> # ℹ 231 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"Find linkage disequilibrium (LD) data given gene. endpoint returns linkage disequilibrium data cis-eQTLs found associated provided gene specified dataset. Results queried gencode ID. default, service queries latest GTEx release. Specify dataset ID fetch results different dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data( gencodeId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(gencodeId = \"ENSG00000132693.12\") #> Warning: ! Total number of items (3558) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 15 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3558 #> # A tibble: 250 × 3 #> variantId_1 variantId_2 ld #> #> 1 chr1_159230230_G_T_b38 chr1_159230339_A_C_b38 1 #> 2 chr1_159230230_G_T_b38 chr1_159245536_C_T_b38 0.971 #> 3 chr1_159230230_G_T_b38 chr1_159302270_T_C_b38 0.717 #> 4 chr1_159230230_G_T_b38 chr1_159343657_A_T_b38 0.302 #> 5 chr1_159230230_G_T_b38 chr1_159344052_G_A_b38 0.300 #> 6 chr1_159230230_G_T_b38 chr1_159347493_G_A_b38 0.300 #> 7 chr1_159230230_G_T_b38 chr1_159350390_C_A_b38 0.300 #> 8 chr1_159230230_G_T_b38 chr1_159351189_G_A_b38 0.300 #> 9 chr1_159230230_G_T_b38 chr1_159359256_C_A_b38 0.302 #> 10 chr1_159230230_G_T_b38 chr1_159360755_ATACATAAGTG_A_b38 0.300 #> # ℹ 240 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Maintenance Message — get_maintenance_message","title":"Get Maintenance Message — get_maintenance_message","text":"Getting maintenance messages database enabled. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"get_maintenance_message(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Maintenance Message — get_maintenance_message","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Maintenance Message — get_maintenance_message","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Maintenance Message — get_maintenance_message","text":"Note typically returns empty tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"# \\dontrun{ get_maintenance_message() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 0 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 0 #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Exon Expression — get_median_exon_expression","title":"Get Median Exon Expression — get_median_exon_expression","text":"Find median exon expression data. Returns median exon read counts, tissues, collapsed gene model. Results may filtered dataset, gene tissue, least one gene must provided default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"get_median_exon_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Exon Expression — get_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Exon Expression — get_median_exon_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"# \\dontrun{ # median exon expression values for CRP, filtered for whole blood get_median_exon_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 8 #> median exonId tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #> #> 1 0 ENSG00000… Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP #> 2 5 ENSG00000… Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP #> # ℹ 1 more variable: unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Gene Expression — get_median_gene_expression","title":"Get Median Gene Expression — get_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"get_median_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Gene Expression — get_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Gene Expression — get_median_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"# \\dontrun{ get_median_gene_expression(gencodeIds = \"ENSG00000132693.12\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 7 #> median tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 0.347 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 0.240 Adipose_Visceral_Omen… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 0.384 Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 0.198 Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 0.332 Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 0.117 Artery_Tibial UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 7 0.631 Bladder UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 8 0.0347 Brain_Amygdala UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 44 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Junction Expression — get_median_junction_expression","title":"Get Median Junction Expression — get_median_junction_expression","text":"Find junction gene expression data. Returns median junction read counts tissues given gene known transcripts. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"get_median_junction_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Junction Expression — get_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Junction Expression — get_median_junction_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"# \\dontrun{ get_median_junction_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #> median junctionId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 2 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 3 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 4 0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 5 0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 6 0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 7 0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 8 0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 9 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 10 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol , unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Transcript Expression — get_median_transcript_expression","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"Find median transcript expression data known transcripts gene. Returns median normalized expression tissues known transcripts given gene. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"get_median_transcript_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"# \\dontrun{ get_median_transcript_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #> median transcriptId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0.130 ENST00000255030.9 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 2 0 ENST00000368110.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 3 0 ENST00000368111.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 4 0 ENST00000368112.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 5 0 ENST00000437342.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 6 0.0100 ENST00000473196.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 7 0 ENST00000489317.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 9 0 ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 10 0 ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol , unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"Find multi-tissue eQTL Metasoft results. service returns multi-tissue eQTL Metasoft results given gene variant specified dataset. Versioned GENCODE ID must provided. tissue, results include: m-value (mValue), normalized effect size (nes), p-value (pValue), standard error (se). m-value posterior probability eQTL effect exists tissue tested cross-tissue meta-analysis (Han Eskin, PLoS Genetics 8(3): e1002555, 2012). normalized effect size slope linear regression normalized expression data versus three genotype categories using single-tissue eQTL analysis, representing eQTL effect size. p-value t-test compares observed NES single-tissue eQTL analysis null NES 0. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"get_multi_tissue_eqtls( gencodeIds, variantId = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_multi_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 132 #> # A tibble: 6,468 × 5 #> gencodeId datasetId metaP variantId tissues #> #> 1 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 2 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 3 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 4 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 5 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 6 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 7 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 8 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 9 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 10 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> # ℹ 6,458 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Neighbor Gene — get_neighbor_gene","title":"Get Neighbor Gene — get_neighbor_gene","text":"Find neighboring genes certain chromosome around position certain window size. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"get_neighbor_gene(pos, chromosome, bp_window, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Neighbor Gene — get_neighbor_gene","text":"pos Integer, vector. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". bp_window Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Neighbor Gene — get_neighbor_gene","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"# \\dontrun{ get_neighbor_gene(pos = 1000000, chromosome = \"chr1\", bp_window = 10000) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 15 #> chromosome dataSource description end gencodeId gencodeVersion geneStatus #> #> 1 chr1 HAVANA novel transc… 9.98e5 ENSG0000… v26 \"\" #> 2 chr1 HAVANA hes family b… 1.00e6 ENSG0000… v26 \"\" #> 3 chr1 HAVANA ISG15 ubiqui… 1.01e6 ENSG0000… v26 \"\" #> 4 chr1 HAVANA ribosomal pr… 1.01e6 ENSG0000… v26 \"\" #> # ℹ 8 more variables: geneSymbol , geneSymbolUpper , geneType , #> # genomeBuild , start , strand , tss , entrezGeneId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":null,"dir":"Reference","previous_headings":"","what":"Get News Item — get_news_item","title":"Get News Item — get_news_item","text":"Getting news items database current. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get News Item — get_news_item","text":"","code":"get_news_item(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get News Item — get_news_item","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get News Item — get_news_item","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get News Item — get_news_item","text":"","code":"# \\dontrun{ get_news_item() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 23 #> # A tibble: 23 × 6 #> title newsText rank dateCreated release id #> #> 1 New Top 50 Expressed Genes Visualiz… \"The GT… 240 2018-04-04 news_i… 240 #> 2 New Multi-Gene Query Visualization \"The GT… 250 2018-04-04 news_i… 250 #> 3 New eQTL Dashboard Visualization \"The GT… 260 2018-04-04 news_i… 260 #> 4 Video Tutorial for the Gene-eQTL Vi… \"Watch … 270 2018-04-05 news_i… 270 #> 5 Access GTEx Biospecimens Here \"We hav… 280 2018-05-10 news_i… 280 #> 6 Access GTEx Data Programmatically w… \"You ca… 290 2018-09-20 news_i… 290 #> 7 Reuse GTEx Visualizations On Your W… \"You ca… 300 2018-09-20 news_i… 300 #> 8 Use The GTEx Portal On Your Phone \"We hav… 310 2018-09-20 news_i… 310 #> 9 GTEx Portal Visualizations Updated \"We hav… 320 2018-12-06 news_i… 320 #> 10 Help Us Help You: New Feature Survey \"PLEASE… 331 2019-02-06 news_i… 331 #> # ℹ 13 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Biobank Data) — get_sample_biobank_data","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"get_sample_biobank_data( draw = NULL, materialTypes = NULL, tissueSiteDetailIds = NULL, pathCategory = NULL, tissueSampleIds = NULL, sex = NULL, sortBy = \"sampleId\", sortDirection = \"asc\", searchTerm = NULL, sampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"draw Integer. materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"# \\dontrun{ get_sample_biobank_data(tissueSiteDetailIds = \"Whole_Blood\") #> Warning: ! Total number of items (1329) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems (recordsFiltered) = 1329 #> • recordsTotal = 72513 #> # A tibble: 250 × 26 #> materialType sampleId sampleIdUpper sex hasGTExImage concentration #> #> 1 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 190. #> 2 RNA:Total RNA GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 154 #> 3 RNA:Total RNA GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 41.2 #> 4 DNA:DNA Genomic GTEX-111CU-00… GTEX-111CU-0… male FALSE 85.9 #> 5 RNA:Total RNA GTEX-111CU-00… GTEX-111CU-0… male FALSE 96.0 #> 6 RNA:Total RNA GTEX-111CU-00… GTEX-111CU-0… male FALSE 95.3 #> 7 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male FALSE 142. #> 8 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male FALSE 4.35 #> 9 RNA:Total RNA GTEX-111FC-00… GTEX-111FC-0… male FALSE 128. #> 10 RNA:Total RNA GTEX-111FC-00… GTEX-111FC-0… male FALSE 128. #> # ℹ 240 more rows #> # ℹ 20 more variables: analysisRelease , genotype , hardyScale , #> # pathologyNotes , subjectId , tissueSiteDetailId , #> # hasGenotype , originalMaterialType , aliquotId , #> # tissueSampleId , ageBracket , brainTissueDonor , #> # volume , hasExpressionData , hasBRDImage , #> # tissueSiteDetail , amount , mass , tissueSite , … # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"service returns information samples used analyses datasets. Results may filtered dataset ID, sample ID, subject ID, sample metadata, provided parameters. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"get_sample_datasets_endpoints( datasetId = \"gtex_v8\", sampleIds = NULL, tissueSampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, sex = NULL, pathCategory = NULL, tissueSiteDetailId = NULL, aliquotIds = NULL, autolysisScores = NULL, hardyScales = NULL, ischemicTime = NULL, ischemicTimeGroups = NULL, rin = NULL, uberonIds = NULL, dataTypes = NULL, sortBy = NULL, sortDirection = NULL, page = NULL, itemsPerPage = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleIds Character vector. GTEx sample ID. tissueSampleIds Array strings. list Tissue Sample ID(s). subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". sex String. Options: \"male\", \"female\". pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. aliquotIds Character vector. autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". rin Integer vector. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"# \\dontrun{ get_sample_datasets_endpoints() #> Warning: ! Total number of items (22734) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 91 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 22734 #> # A tibble: 10,946 × 20 #> ischemicTime aliquotId tissueSampleId tissueSiteDetail dataType #> #> 1 1188 SM-58Q7G GTEX-1117F-0003 Whole Blood WES #> 2 1188 SM-5DWSB GTEX-1117F-0003 Whole Blood OMNI #> 3 1188 SM-6WBT7 GTEX-1117F-0003 Whole Blood WGS #> 4 1193 SM-AHZ7F GTEX-1117F-0011-R10a Brain - Frontal Cortex … NA #> 5 1193 SM-CYKQ8 GTEX-1117F-0011-R10b Brain - Frontal Cortex … NA #> 6 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 7 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 8 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 9 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 10 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> # ℹ 10,936 more rows #> # ℹ 15 more variables: ischemicTimeGroup , freezeType , #> # sampleId , sampleIdUpper , ageBracket , hardyScale , #> # tissueSiteDetailId , subjectId , uberonId , sex , #> # datasetId , rin , pathologyNotesCategories , #> # pathologyNotes , autolysisScore # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Service Info — get_service_info","title":"Get Service Info — get_service_info","text":"General information GTEx service. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Service Info — get_service_info","text":"","code":"get_service_info()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Service Info — get_service_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Service Info — get_service_info","text":"","code":"# \\dontrun{ get_service_info() #> # A tibble: 1 × 9 #> id name version organization_name organization_url description contactUrl #> #> 1 org.g… GTEx… 2.0.0 GTEx Project https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl , environment # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Find significant single tissue eQTLs. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, gene, variant dataset. search gene, use versioned GENCODE ID. search variant, use dbSNP rs ID (snpId). default, service queries latest GTEx release retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"get_significant_single_tissue_eqtls( gencodeIds = NULL, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Note: although GTEx Portal API documentation says use dbSNP rsID searching variant, returns results. Instead use gtex variant IDs e.g. use \"chr1_153209640_C_A_b38\" instead \"rs1410858\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs12128960 159343657 RS12128960 chr1_1593… CRP 8.52e-5 CRP #> 2 rs12132451 159344052 RS12132451 chr1_1593… CRP 7.92e-5 CRP #> 3 rs12136402 159347493 RS12136402 chr1_1593… CRP 7.92e-5 CRP #> 4 rs10908709 159350390 RS10908709 chr1_1593… CRP 7.92e-5 CRP #> 5 rs10908710 159351189 RS10908710 chr1_1593… CRP 7.92e-5 CRP #> 6 rs11265178 159359256 RS11265178 chr1_1593… CRP 9.62e-5 CRP #> 7 rs35532309 159360755 RS35532309 chr1_1593… CRP 6.11e-5 CRP #> 8 rs6692378 159369451 RS6692378 chr1_1593… CRP 1.17e-6 CRP #> 9 rs10908714 159370563 RS10908714 chr1_1593… CRP 1.80e-5 CRP #> 10 rs6656924 159372915 RS6656924 chr1_1593… CRP 1.00e-6 CRP #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes # search by variant - must be variantId (not rsid) get_significant_single_tissue_eqtls(variantIds = \"chr1_153209640_C_A_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs1410858 153209640 RS1410858 chr1_15320… LOR 5.47e- 5 LOR #> 2 rs1410858 153209640 RS1410858 chr1_15320… PRR9 5.35e-19 PRR9 #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes # filter by gene/variant and tissue site - either `gencodeIds` or `variantIds` # should be supplied as a minimum get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), variantIds = \"chr1_153209640_C_A_b38\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper datasetId #> #> 1 rs14… 1.53e8 RS1410858 chr1_153… LOR 5.47e-5 LOR gtex_v8 #> # ℹ 5 more variables: tissueSiteDetailId , ontologyId , #> # chromosome , gencodeId , nes # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"Find significant single tissue eQTLs using Chromosomal Locations. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, /dataset. default, service queries latest GTEx release. Since endpoint used support third party program portal, return structure different endpoints paginated. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"get_significant_single_tissue_eqtls_by_location( tissueSiteDetailId, start, end, chromosome, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"# \\dontrun{ get_significant_single_tissue_eqtls_by_location( tissueSiteDetailId = \"Artery_Aorta\", start = 10000, end = 250000, chromosome = \"chr11\") #> # A tibble: 434 × 11 #> chromosome datasetId gencodeId geneSymbol geneSymbolUpper nes pValue #> #> 1 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.381 1.11e- 6 #> 2 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.364 2.25e- 6 #> 3 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.417 3.10e- 8 #> 4 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.480 8.39e- 9 #> 5 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> 6 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.553 8.89e-10 #> 7 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.577 2.95e-12 #> 8 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.547 6.13e-10 #> 9 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> 10 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> # ℹ 424 more rows #> # ℹ 4 more variables: pos , snpId , tissueSiteDetailId , #> # variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"Retrieve Interaction eQTL Data. service returns cell type interaction eQTLs (ieQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"get_significant_single_tissue_ieqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_ieqtls(c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 86 #> # A tibble: 86 × 24 #> snpId bGISE pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #> #> 1 rs34188… 0.0890 1.54e8 RS34188388 0.102 0.00447 LOR LOR #> 2 rs24945… 0.0654 1.60e8 RS2494523 0.867 0.00129 CRP CRP #> 3 rs986760 0.148 1.53e8 RS986760 0.0454 0.00694 LOR LOR #> 4 rs17697… 0.0428 1.59e8 RS17697329 0.515 0.000627 CRP CRP #> 5 rs67415… 0.154 1.53e8 RS67415955 0.565 0.000754 LOR LOR #> 6 rs12133… 0.157 1.60e8 RS12133356 0.634 0.00106 CRP CRP #> 7 rs12132… 0.113 1.53e8 RS12132927 0.858 0.00365 LOR LOR #> 8 rs30269… 0.0683 1.59e8 RS3026943 0.684 0.00222 CRP CRP #> 9 rs24946… 0.0567 1.54e8 RS2494670 0.516 0.000595 LOR LOR #> 10 rs12121… 0.0695 1.60e8 RS12121609 0.444 0.000266 CRP CRP #> # ℹ 76 more rows #> # ℹ 16 more variables: pValueI , bGI , tissueSiteDetailId , #> # ontologyId , chromosome , tissueCellType , #> # tssDistance , bGSE , variantId , maf , bISE , #> # datasetId , bG , pValueAdjustedBH , bI , #> # gencodeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"Retrieve Interaction sQTL Data. service retrieves cell type interaction sQTLs (isQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"get_significant_single_tissue_isqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_isqtls(gencodeIds = c(\"ENSG00000065613.9\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 25 #> snpId bGISE pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #> #> 1 rs4845790 0.0194 1.53e8 RS4845790 0.00645 8.97e-7 LOR LOR #> 2 rs4845790 0.0196 1.53e8 RS4845790 0.0118 1.41e-7 LOR LOR #> 3 rs359327… 0.0289 1.54e8 RS35932716 0.0142 3.70e-5 LOR LOR #> 4 rs146285… 0.0293 1.53e8 RS1462851… 0.0225 3.03e-5 LOR LOR #> # ℹ 17 more variables: pValueI , bGI , tissueSiteDetailId , #> # ontologyId , chromosome , tissueCellType , #> # tssDistance , bGSE , variantId , maf , bISE , #> # datasetId , bG , pValueAdjustedBH , bI , #> # gencodeId , phenotypeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"Retrieve Single Tissue sQTL Data. service returns single tissue sQTL data given genes, specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"get_significant_single_tissue_sqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_sqtls(gencodeIds = c(\"ENSG00000065613.9\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 176 #> # A tibble: 176 × 14 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs4636462 152442732 RS4636462 chr1_1524… LOR 7.71e-5 LOR #> 2 rs4845768 152442997 RS4845768 chr1_1524… LOR 6.57e-5 LOR #> 3 rs12069640 152444300 RS12069640 chr1_1524… LOR 7.13e-5 LOR #> 4 rs11803629 152445670 RS11803629 chr1_1524… LOR 1.81e-4 LOR #> 5 rs12125681 152445737 RS12125681 chr1_1524… LOR 1.81e-4 LOR #> 6 rs11205004 152446586 RS11205004 chr1_1524… LOR 1.81e-4 LOR #> 7 rs11579085 152447965 RS11579085 chr1_1524… LOR 1.81e-4 LOR #> 8 rs1885529 152448570 RS1885529 chr1_1524… LOR 1.81e-4 LOR #> 9 rs1885528 152448978 RS1885528 chr1_1524… LOR 1.81e-4 LOR #> 10 rs1885527 152449069 RS1885527 chr1_1524… LOR 1.81e-4 LOR #> # ℹ 166 more rows #> # ℹ 7 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes , #> # phenotypeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleux Gex — get_single_nucleus_gex","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"Retrieve Single Nucleus Gene Expression Data given Gene. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"get_single_nucleus_gex( gencodeIds, datasetId = \"gtex_snrnaseq_pilot\", tissueSiteDetailIds = NULL, excludeDataArray = TRUE, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. excludeDataArray String. Options TRUE FALSE page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"# \\dontrun{ # Search for one or more genes - returns a tibble with one row per tissue. # Column \"cellTypes\" now contains a tibble of expression summary data, with # one row for each cell type get_single_nucleus_gex(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 14 #> # A tibble: 14 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol cellTypes unit #> #> 1 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 2 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 3 Esophagus_Mucosa UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 4 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 5 Lung UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 6 Prostate UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 7 Skin_Sun_Exposed_L… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 8 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 9 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 10 Esophagus_Mucosa UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 11 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 12 Heart_Left_Ventric… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 13 Lung UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 14 Prostate UBERON:00… gtex_snr… ENSG0000… CRP log(… # `excludeDataArray = FALSE` - expression values are stored under \"celltypes\" # in an additional column called \"data\" response <- get_single_nucleus_gex(gencodeIds = \"ENSG00000132693.12\", excludeDataArray = FALSE, itemsPerPage = 2) #> Warning: ! Total number of items (7) exceeds maximum page size (2). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 2 #> • totalNumberOfItems = 7 response #> # A tibble: 2 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol cellTypes unit #> #> 1 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 2 Breast_Mammary_Tiss… UBERON:00… gtex_snr… ENSG0000… CRP log(… # \"cellTypes\" contains a tibble of data with one row for each # cell type e.g. for Breast_Mammary_Tissue response$cellTypes[[2]] #> # A tibble: 2 × 8 #> cellType count meanWithZeros meanWithoutZeros medianWithZeros #> #> 1 Epithelial cell (luminal) 2 0.000902 2.19 0 #> 2 Endothelial cell (vascul… 1 0.00401 3.05 0 #> # ℹ 3 more variables: medianWithoutZeros , numZeros , data # when `excludeDataArray = FALSE`, expression values are stored in \"data\" # e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal): response$cellTypes[[2]]$data[[1]] #> [1] 1.593315 2.782725 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"Retrieve Summarized Single Nucleus Gene Expression Data. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"get_single_nucleus_gex_summary( datasetId = \"gtex_snrnaseq_pilot\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"# \\dontrun{ # all tissues get_single_nucleus_gex_summary() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 114 #> # A tibble: 114 × 5 #> tissueSiteDetailId ontologyId datasetId cellType numCells #> #> 1 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. … 769 #> 2 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (NMJ-… 95 #> 3 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Endothelial c… 1124 #> 4 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. … 20772 #> 5 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Fibroblast 5944 #> 6 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Pericyte/SMC 448 #> 7 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Immune (DC/ma… 721 #> 8 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Adipocyte 159 #> 9 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Schwann cell 35 #> 10 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Satellite cell 487 #> # ℹ 104 more rows # filter for specific tissue get_single_nucleus_gex_summary(tissueSiteDetailIds = c(\"Breast_Mammary_Tissue\", \"Skin_Sun_Exposed_Lower_leg\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25 #> # A tibble: 25 × 5 #> tissueSiteDetailId ontologyId datasetId cellType numCells #> #> 1 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Epithel… 4849 #> 2 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Adipocy… 1761 #> 3 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Immune … 358 #> 4 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Myoepit… 950 #> 5 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Fibrobl… 819 #> 6 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Endothe… 762 #> 7 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Endothe… 119 #> 8 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Pericyt… 152 #> 9 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Sweat g… 300 #> 10 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Epithel… 72 #> # ℹ 15 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sqtl Genes — get_sqtl_genes","title":"Get Sqtl Genes — get_sqtl_genes","text":"Retrieve sGenes (sQTL Genes). service returns sGenes (sQTL Genes) specified dataset. Results may filtered tissue. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"get_sqtl_genes( tissueSiteDetailId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sqtl Genes — get_sqtl_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sqtl Genes — get_sqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"# \\dontrun{ get_sqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (3013) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 13 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3013 #> # A tibble: 250 × 11 #> nPhenotypes pValueThreshold phenotypeId geneSymbol pValue datasetId #> #> 1 9 0.0000145 chr1:15947:16607:… WASH7P 7.15e- 8 gtex_v8 #> 2 6 0.00000634 chr1:1090428:1091… C1orf159 6.85e- 10 gtex_v8 #> 3 7 0.00000908 chr1:1228946:1231… SDF4 1.16e-188 gtex_v8 #> 4 6 0.00000861 chr1:1310688:1310… PUSL1 2.50e- 40 gtex_v8 #> 5 3 0.00000954 chr1:1325102:1327… CPTP 9.60e- 7 gtex_v8 #> 6 2 0.0000147 chr1:1487914:1489… ATAD3C 1.61e- 25 gtex_v8 #> 7 5 0.00000740 chr1:1487914:1489… ATAD3B 1.61e- 25 gtex_v8 #> 8 2 0.0000361 chr1:1545002:1547… SSU72 3.28e- 25 gtex_v8 #> 9 19 0.00000176 chr1:1629311:1629… MIB2 1.97e- 12 gtex_v8 #> 10 8 0.00000273 chr1:1641113:1641… CDK11B 3.08e- 56 gtex_v8 #> # ℹ 240 more rows #> # ℹ 5 more variables: empiricalPValue , tissueSiteDetailId , #> # ontologyId , qValue , gencodeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Subject — get_subject","title":"Get Subject — get_subject","text":"service returns information subjects used analyses datasets. Results may filtered dataset ID, subject ID, sex, age bracket Hardy Scale. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Subject — get_subject","text":"","code":"get_subject( datasetId = \"gtex_v8\", sex = NULL, ageBrackets = NULL, hardyScales = NULL, subjectIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Subject — get_subject","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sex String. Options: \"male\", \"female\". ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". subjectIds Character vector. GTEx subject ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Subject — get_subject","text":"Tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Subject — get_subject","text":"","code":"# \\dontrun{ get_subject() #> Warning: ! Total number of items (979) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 979 #> # A tibble: 250 × 5 #> hardyScale ageBracket subjectId sex datasetId #> #> 1 Slow death 60-69 GTEX-1117F female gtex_v8 #> 2 Ventilator case 50-59 GTEX-111CU male gtex_v8 #> 3 Fast death - violent 60-69 GTEX-111FC male gtex_v8 #> 4 Intermediate death 60-69 GTEX-111VG male gtex_v8 #> 5 Ventilator case 60-69 GTEX-111YS male gtex_v8 #> 6 Ventilator case 60-69 GTEX-1122O female gtex_v8 #> 7 Fast death - natural causes 60-69 GTEX-1128S female gtex_v8 #> 8 NA 60-69 GTEX-113IC male gtex_v8 #> 9 Fast death - natural causes 50-59 GTEX-113JC female gtex_v8 #> 10 Fast death - natural causes 60-69 GTEX-117XS male gtex_v8 #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Tissue Site Detail — get_tissue_site_detail","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"Retrieve tissue site detail information database GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"get_tissue_site_detail(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"# \\dontrun{ # returns a tibble with one row per tissue get_tissue_site_detail() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 18 #> tissueSiteDetailId colorHex colorRgb datasetId eGeneCount expressedGeneCount #> #> 1 Adipose_Subcutaneo… FF6600 255,102… gtex_v8 15607 28830 #> 2 Adipose_Visceral_O… FFAA00 255,170… gtex_v8 12482 28881 #> 3 Adrenal_Gland 33DD33 51,221,… gtex_v8 8123 28235 #> 4 Artery_Aorta FF5555 255,85,… gtex_v8 12493 28025 #> 5 Artery_Coronary FFAA99 255,170… gtex_v8 6296 28462 #> 6 Artery_Tibial FF0000 255,0,0 gtex_v8 15008 27217 #> 7 Bladder AA0000 170,0,0 gtex_v8 NA 28949 #> 8 Brain_Amygdala EEEE00 238,238… gtex_v8 3726 28196 #> 9 Brain_Anterior_cin… EEEE00 238,238… gtex_v8 5640 28921 #> 10 Brain_Caudate_basa… EEEE00 238,238… gtex_v8 8362 29230 #> # ℹ 44 more rows #> # ℹ 12 more variables: hasEGenes , hasSGenes , mappedInHubmap , #> # eqtlSampleSummary , rnaSeqSampleSummary , sGeneCount , #> # samplingSite , tissueSite , tissueSiteDetail , #> # tissueSiteDetailAbbr , ontologyId , ontologyIri # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns bladder_site_details <- get_tissue_site_detail() |> dplyr::filter(tissueSiteDetailId == \"Bladder\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 purrr::pluck(bladder_site_details, \"eqtlSampleSummary\", 1) #> $totalCount #> [1] 21 #> #> $female #> $female$ageMax #> [1] 59 #> #> $female$ageMin #> [1] 27 #> #> $female$ageMean #> [1] 43.6 #> #> $female$count #> [1] 7 #> #> #> $male #> $male$ageMax #> [1] 61 #> #> $male$ageMin #> [1] 21 #> #> $male$ageMean #> [1] 46 #> #> $male$count #> [1] 14 #> #> purrr::pluck(bladder_site_details, \"rnaSeqSampleSummary\", 1) #> $totalCount #> [1] 21 #> #> $female #> $female$ageMax #> [1] 59 #> #> $female$ageMin #> [1] 27 #> #> $female$ageMean #> [1] 43.6 #> #> $female$count #> [1] 7 #> #> #> $male #> $male$ageMax #> [1] 61 #> #> $male$ageMin #> [1] 21 #> #> $male$ageMean #> [1] 46 #> #> $male$count #> [1] 14 #> #> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Top Expressed Genes — get_top_expressed_genes","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"Find top expressed genes specified tissue. Returns top expressed genes specified tissue dataset, sorted median expression. optional parameter filterMtGene set true, mitochondrial genes excluded results. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"get_top_expressed_genes( tissueSiteDetailId, datasetId = \"gtex_v8\", filterMtGene = TRUE, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". filterMtGene Logical. Exclude mitochondrial genes. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"# \\dontrun{ get_top_expressed_genes(tissueSiteDetailId = \"Artery_Aorta\") #> Warning: ! Total number of items (56163) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 225 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 56163 #> # A tibble: 250 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol median unit #> #> 1 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… MGP 11936. TPM #> 2 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… FTL 9196. TPM #> 3 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… ACTB 9154. TPM #> 4 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… BGN 8167. TPM #> 5 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… TAGLN 6099. TPM #> 6 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… ACTA2 5736. TPM #> 7 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… IGFBP7 5639. TPM #> 8 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… MYL9 4275. TPM #> 9 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… HSPB1 3780. TPM #> 10 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… FLNA 3732. TPM #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Transcripts — get_transcripts","title":"Get Transcripts — get_transcripts","text":"Find transcripts reference gene. service returns information transcripts given versioned GENCODE ID. genome build GENCODE version must provided. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Transcripts — get_transcripts","text":"","code":"get_transcripts( gencodeId, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Transcripts — get_transcripts","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Transcripts — get_transcripts","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Transcripts — get_transcripts","text":"","code":"# \\dontrun{ get_transcripts(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 11 #> start end featureType genomeBuild transcriptId source chromosome gencodeId #> #> 1 1.53e8 1.53e8 transcript GRCh38/hg38 ENST0000036… HAVANA chr1 ENSG0000… #> # ℹ 3 more variables: geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant — get_variant","title":"Get Variant — get_variant","text":"service returns information variant, including position, dbSNP RS ID, reference allele, alternative allele, whether minor allele frequency >= 1%. GTEx v6p, also information whether whole exome sequence chip sequencing data available. Results may queried GTEx variant ID (variantId), dbSNP RS ID (snpId) genomic location (chromosome pos). Variants identified based genotype data dataset cohort, namely, dataset-dependent. variant assigned unique GTEx variant ID (.e. primary key). variants mappable dbSNP RS ID. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant — get_variant","text":"","code":"get_variant( snpId = NULL, variantId = NULL, chromosome = NULL, pos = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant — get_variant","text":"snpId String variantId String. gtex variant ID. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". pos Integer, vector. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant — get_variant","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant — get_variant","text":"","code":"# search by rsid get_variant(snpId = \"rs1410858\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> # ℹ 2 more variables: datasetId , ref # search by variantId get_variant(variantId = \"chr1_153209640_C_A_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> # ℹ 2 more variables: datasetId , ref # search by chromosome and position get_variant(chromosome = \"chr1\", pos = 153209600:153209700) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs11205220 1_153182115_T_… 1.53e8 TRUE chr1_153… C chr1 RS11205220 #> 2 rs1410858 1_153182116_C_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T chr1 RS1392967… #> 4 rs80104092 1_153182149_T_… 1.53e8 FALSE chr1_153… C chr1 RS80104092 #> # ℹ 2 more variables: datasetId , ref "},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant By Location — get_variant_by_location","title":"Get Variant By Location — get_variant_by_location","text":"service allows user query information variants certain chromosome certain location. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location( start, end, chromosome, sortBy = \"pos\", sortDirection = \"asc\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant By Location — get_variant_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant By Location — get_variant_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(start = 153209600, end = 153209700, chromosome = \"chr1\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs11205220 1_153182115_T_… 1.53e8 TRUE chr1_153… C chr1 RS11205220 #> 2 rs1410858 1_153182116_C_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T chr1 RS1392967… #> 4 rs80104092 1_153182149_T_… 1.53e8 FALSE chr1_153… C chr1 RS80104092 #> # ℹ 2 more variables: datasetId , ref "},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr: Query the GTEx Portal API — gtexr-package","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"convenient R interface Genotype-Tissue Expression (GTEx) Portal API. information API, see https://gtexportal.org/api/v2/redoc.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"Maintainer: Alasdair Warwick alasdair.warwick.19@ucl.ac.uk (ORCID) [copyright holder] Authors: Benjamin Zuckerman (ORCID) Abraham Olvera-Barrios (ORCID) Chuin Ying Ung (ORCID) Robert Luben (ORCID)","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr arguments — gtexr_arguments","title":"gtexr arguments — gtexr_arguments","text":"Internal function documents arguments exported gtexr functions wrap GTEx Portal API endpoints (using roxygen @inheritParams tag).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gtexr arguments — gtexr_arguments","text":"","code":"gtexr_arguments( ageBrackets = NULL, aliquotIds = NULL, attributeSubset = NULL, autolysisScores = NULL, cellType = NULL, bp_window = NULL, chromosome = NULL, datasetId = NULL, dataTypes = NULL, draw = NULL, end = NULL, excludeDataArray = NULL, .featureId = NULL, filterMtGene = NULL, gencodeId = NULL, gencodeIds = NULL, gencodeVersion = NULL, geneId = NULL, geneIds = NULL, genomeBuild = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL, itemsPerPage = NULL, ischemicTime = NULL, ischemicTimeGroups = NULL, materialTypes = NULL, organizationName = NULL, page = NULL, pathCategory = NULL, phenotypeId = NULL, pos = NULL, project_id = NULL, rin = NULL, sampleId = NULL, sampleIds = NULL, searchTerm = NULL, sex = NULL, snpId = NULL, sortBy = NULL, sortDirection = NULL, start = NULL, subjectIds = NULL, tissueSampleIds = NULL, tissueSiteDetailId = NULL, tissueSiteDetailIds = NULL, uberonIds = NULL, variantId = NULL, variantIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gtexr arguments — gtexr_arguments","text":"ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". aliquotIds Character vector. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". bp_window Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". draw Integer. end Integer. excludeDataArray String. Options TRUE FALSE .featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. filterMtGene Logical. Exclude mitochondrial genes. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". geneId String. gene symbol, gencode ID, Ensemble ID. geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. itemsPerPage Integer (default = 250). ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\". page Integer (default = 0). pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". phenotypeId String. See GTEx portal FAQs details. pos Integer, vector. project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\". rin Integer vector. sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ sampleIds Character vector. GTEx sample ID. searchTerm String. sex String. Options: \"male\", \"female\". snpId String sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". start Integer. subjectIds Character vector. GTEx subject ID. tissueSampleIds Array strings. list Tissue Sample ID(s). tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). variantId String. gtex variant ID. variantIds Character vector. Gtex variant IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gtexr arguments — gtexr_arguments","text":"Returns NULL invisibly. Used documentation .","code":""},{"path":"https://rmgpanw.github.io/gtexr/news/index.html","id":"gtexr-development-version","dir":"Changelog","previous_headings":"","what":"gtexr (development version)","title":"gtexr (development version)","text":"Added NEWS.md file track changes package.","code":""}] +[{"path":"https://rmgpanw.github.io/gtexr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 gtexr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/developer_guide.html","id":"functions","dir":"Articles","previous_headings":"","what":"Functions","title":"Developer guide","text":"Function name title API endpoint lower case, words separated underscores. @description section copied verbatim API documentation site ends link corresponding API endpoint documentation. notes may added @details. Names match API endpoint, except argument accepts array (vector R) values, case pluralised.1 Default values also match API endpoint. Query parameters flagged “required” GTEx Portal API documentation default values.2 documented gtexr_arguments.R. functions therefore use @inheritParams gtexr_arguments documentation. Use @family roxygen tag match categories API documentation. used categorise functions pkgdown site reference page. Return tibble. first example @examples must produce output single function call without assignment (e.g. get_news_items(), x <- get_news_items()). used pre-populate argument values gtexr shiny app working example. examples surrounded \\dontrun{}.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"shiny-app","dir":"Articles","previous_headings":"","what":"Shiny app","title":"Introduction to gtexr","text":"Users can try functions interatively ⭐gtexr shiny app⭐, pre-populates query parameters first working example function’s documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"Introduction to gtexr","text":"rest vignette outlines example applications gtexr.","code":"library(gtexr) library(dplyr) library(purrr)"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-build-37-coordinates-for-a-variant","dir":"Articles","previous_headings":"Examples","what":"Get build 37 coordinates for a variant","title":"Introduction to gtexr","text":"","code":"get_variant(snpId = \"rs1410858\") |> tidyr::separate( col = b37VariantId, into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\", remove = FALSE ) |> select(snpId:genome_build) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #> snpId b37VariantId chromosome position reference_allele alternative_allele #> #> 1 rs1410858 1_153182116… 1 1531821… C A #> # ℹ 1 more variable: genome_build "},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-gene-symbol-to-versioned-gencode-id","dir":"Articles","previous_headings":"Examples","what":"Convert gene symbol to versioned GENCODE ID","title":"Introduction to gtexr","text":"Use get_gene() get_genes()","code":"get_genes(\"CRP\") |> select(geneSymbol, gencodeId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #> geneSymbol gencodeId #> #> 1 CRP ENSG00000132693.12"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"convert-rsid-to-gtex-variant-id","dir":"Articles","previous_headings":"Examples","what":"Convert rsID to GTEx variant ID","title":"Introduction to gtexr","text":"Use get_variant()","code":"get_variant(snpId = \"rs1410858\") |> select(snpId, variantId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 2 #> snpId variantId #> #> 1 rs1410858 chr1_153209640_C_A_b38"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"for-a-gene-of-interest-which-tissues-have-significant-cis-eqtls","dir":"Articles","previous_headings":"Examples","what":"For a gene of interest, which tissues have significant cis-eQTLs?","title":"Introduction to gtexr","text":"Use get_significant_single_tissue_eqtls() (note requires versioned GENCODE IDs)","code":"gene_symbol_of_interest <- \"CRP\" gene_gencodeId_of_interest <- get_genes(gene_symbol_of_interest) |> pull(gencodeId) |> suppressMessages() gene_gencodeId_of_interest |> get_significant_single_tissue_eqtls() |> distinct(geneSymbol, gencodeId, tissueSiteDetailId) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 93 #> # A tibble: 3 × 3 #> geneSymbol gencodeId tissueSiteDetailId #> #> 1 CRP ENSG00000132693.12 Thyroid #> 2 CRP ENSG00000132693.12 Esophagus_Gastroesophageal_Junction #> 3 CRP ENSG00000132693.12 Muscle_Skeletal"},{"path":"https://rmgpanw.github.io/gtexr/articles/gtexr.html","id":"get-data-for-non-eqtl-variants","dir":"Articles","previous_headings":"Examples","what":"Get data for non-eQTL variants","title":"Introduction to gtexr","text":"analyses (e.g. Mendelian randomisation) require data variants may may significant eQTLs. Use calculate_expression_quantitative_trait_loci() purrr::map() retrieve data multiple variants","code":"variants_of_interest <- c(\"rs12119111\", \"rs6605071\", \"rs1053870\") variants_of_interest |> set_names() |> map( \\(x) calculate_expression_quantitative_trait_loci( tissueSiteDetailId = \"Liver\", gencodeId = \"ENSG00000237973.1\", variantId = x ) ) |> bind_rows(.id = \"rsid\") |> # optionally, reformat output - first extract genomic coordinates and alleles tidyr::separate( col = \"variantId\", into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\" ) |> # ...then ascertain alternative_allele frequency mutate( alt_allele_count = (2 * homoAltCount) + hetCount, total_allele_count = 2 * (homoAltCount + hetCount + homoRefCount), alternative_allele_frequency = alt_allele_count / total_allele_count ) |> select( rsid, beta = nes, se = error, pValue, minor_allele_frequency = maf, alternative_allele_frequency, chromosome:genome_build, tissueSiteDetailId ) #> # A tibble: 3 × 12 #> rsid beta se pValue minor_allele_frequency alternative_allele_f…¹ #> #> 1 rs121191… 0.0270 0.0670 6.88e-1 0.365 0.635 #> 2 rs6605071 -0.601 0.166 3.88e-4 0.0409 0.959 #> 3 rs1053870 0.0247 0.0738 7.38e-1 0.214 0.214 #> # ℹ abbreviated name: ¹​alternative_allele_frequency #> # ℹ 6 more variables: chromosome , position , reference_allele , #> # alternative_allele , genome_build , tissueSiteDetailId "},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Alasdair Warwick. Author, maintainer, copyright holder. Benjamin Zuckerman. Author. Abraham Olvera-Barrios. Author. Chuin Ying Ung. Author. Robert Luben. Author.","code":""},{"path":"https://rmgpanw.github.io/gtexr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Warwick , Zuckerman B, Olvera-Barrios , Ung C, Luben R (2024). gtexr: Query GTEx Portal API. R package version 0.1.0.9000, https://github.com/rmgpanw/gtexr, https://rmgpanw.github.io/gtexr/.","code":"@Manual{, title = {gtexr: Query the GTEx Portal API}, author = {Alasdair Warwick and Benjamin Zuckerman and Abraham Olvera-Barrios and Chuin Ying Ung and Robert Luben}, year = {2024}, note = {R package version 0.1.0.9000, https://github.com/rmgpanw/gtexr}, url = {https://rmgpanw.github.io/gtexr/}, }"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"gtexr-","dir":"","previous_headings":"","what":"Query the GTEx Portal API","title":"Query the GTEx Portal API","text":"goal gtexr provide convenient R interface GTEx Portal API V2. New R? Try ⭐shiny app⭐.","code":""},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Query the GTEx Portal API","text":"can install package CRAN: can install development version gtexr GitHub :","code":"install.packages(\"gtexr\") # install.packages(\"devtools\") devtools::install_github(\"rmgpanw/gtexr\")"},{"path":"https://rmgpanw.github.io/gtexr/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Query the GTEx Portal API","text":"Get general information GTEx service: Retrieve eQTL genes whole blood tissue: Retrieve significant eQTLs one genes:","code":"library(gtexr) get_service_info() #> # A tibble: 1 × 9 #> id name version organization_name organization_url description contactUrl #> #> 1 org.g… GTEx… 2.0.0 GTEx Project https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl , environment get_eqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (12360) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 50 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 12360 #> # A tibble: 250 × 10 #> tissueSiteDetailId ontologyId datasetId empiricalPValue gencodeId geneSymbol #> #> 1 Whole_Blood UBERON:001… gtex_v8 1.05e- 9 ENSG0000… WASH7P #> 2 Whole_Blood UBERON:001… gtex_v8 1.06e-25 ENSG0000… RP11-34P1… #> 3 Whole_Blood UBERON:001… gtex_v8 6.31e- 2 ENSG0000… CICP27 #> 4 Whole_Blood UBERON:001… gtex_v8 8.71e- 9 ENSG0000… RP11-34P1… #> 5 Whole_Blood UBERON:001… gtex_v8 6.01e-20 ENSG0000… RP11-34P1… #> 6 Whole_Blood UBERON:001… gtex_v8 6.96e- 9 ENSG0000… RP11-34P1… #> 7 Whole_Blood UBERON:001… gtex_v8 3.10e- 4 ENSG0000… RP11-34P1… #> 8 Whole_Blood UBERON:001… gtex_v8 1.92e- 3 ENSG0000… ABC7-4304… #> 9 Whole_Blood UBERON:001… gtex_v8 1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood UBERON:001… gtex_v8 7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange , pValue , #> # pValueThreshold , qValue get_significant_single_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs12128960 159343657 RS12128960 chr1_1593… CRP 8.52e-5 CRP #> 2 rs12132451 159344052 RS12132451 chr1_1593… CRP 7.92e-5 CRP #> 3 rs12136402 159347493 RS12136402 chr1_1593… CRP 7.92e-5 CRP #> 4 rs10908709 159350390 RS10908709 chr1_1593… CRP 7.92e-5 CRP #> 5 rs10908710 159351189 RS10908710 chr1_1593… CRP 7.92e-5 CRP #> 6 rs11265178 159359256 RS11265178 chr1_1593… CRP 9.62e-5 CRP #> 7 rs35532309 159360755 RS35532309 chr1_1593… CRP 6.11e-5 CRP #> 8 rs6692378 159369451 RS6692378 chr1_1593… CRP 1.17e-6 CRP #> 9 rs10908714 159370563 RS10908714 chr1_1593… CRP 1.80e-5 CRP #> 10 rs6656924 159372915 RS6656924 chr1_1593… CRP 1.00e-6 CRP #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes "},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Calculate eQTLs service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"calculate_expression_quantitative_trait_loci( tissueSiteDetailId, gencodeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"Notes output: Beta standard error recorded columns nes error respectively (see GTEx FAQs) variantId contains (order) chromosome, position, reference allele, alternative allele human genome build separated underscores. reference alternative alleles \"chr1_13550_G_A_b38\" example \"G\" \"\" respectively. See examples calculate minor alternative allele frequencies. Notes input: Argument variantId also accepts RSIDs.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_expression_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Expression Quantitative Trait Loci — calculate_expression_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\", gencodeId = \"ENSG00000203782.5\", variantId = \"rs79641866\") #> # A tibble: 1 × 15 #> data error gencodeId geneSymbol genotypes hetCount homoAltCount #> #> 1 0.148 ENSG00000… LOR 38 0 #> # ℹ 8 more variables: homoRefCount , maf , nes , pValue , #> # pValueThreshold , tStatistic , tissueSiteDetailId , #> # variantId # unnest list columns with tidyr::unnest() calculate_expression_quantitative_trait_loci(tissueSiteDetailId = \"Whole_Blood\", gencodeId = \"ENSG00000203782.5\", variantId = \"rs79641866\") |> tidyr::unnest(c(\"data\", \"genotypes\")) #> # A tibble: 670 × 15 #> data error gencodeId geneSymbol genotypes hetCount homoAltCount #> #> 1 -1.16 0.148 ENSG00000203782.5 LOR 0 38 0 #> 2 0.978 0.148 ENSG00000203782.5 LOR 0 38 0 #> 3 0.0542 0.148 ENSG00000203782.5 LOR 0 38 0 #> 4 -0.278 0.148 ENSG00000203782.5 LOR 0 38 0 #> 5 0.182 0.148 ENSG00000203782.5 LOR 1 38 0 #> 6 -0.614 0.148 ENSG00000203782.5 LOR 0 38 0 #> 7 0.462 0.148 ENSG00000203782.5 LOR 0 38 0 #> 8 -0.125 0.148 ENSG00000203782.5 LOR 0 38 0 #> 9 0.421 0.148 ENSG00000203782.5 LOR 0 38 0 #> 10 0.274 0.148 ENSG00000203782.5 LOR 0 38 0 #> # ℹ 660 more rows #> # ℹ 8 more variables: homoRefCount , maf , nes , pValue , #> # pValueThreshold , tStatistic , tissueSiteDetailId , #> # variantId # to calculate minor and alternative allele frequencies calculate_expression_quantitative_trait_loci( tissueSiteDetailId = \"Liver\", gencodeId = \"ENSG00000237973.1\", variantId = \"rs12119111\" ) |> dplyr::bind_rows(.id = \"rsid\") |> tidyr::separate( col = \"variantId\", into = c( \"chromosome\", \"position\", \"reference_allele\", \"alternative_allele\", \"genome_build\" ), sep = \"_\" ) |> # ...then ascertain alternative_allele frequency dplyr::mutate( alt_allele_count = (2 * homoAltCount) + hetCount, total_allele_count = 2 * (homoAltCount + hetCount + homoRefCount), alternative_allele_frequency = alt_allele_count / total_allele_count ) |> dplyr::select( rsid, beta = nes, se = error, pValue, minor_allele_frequency = maf, alternative_allele_frequency, chromosome:genome_build, tissueSiteDetailId ) #> # A tibble: 1 × 12 #> rsid beta se pValue minor_allele_frequency alternative_allele_frequency #> #> 1 1 0.0270 0.0670 0.688 0.365 0.635 #> # ℹ 6 more variables: chromosome , position , reference_allele , #> # alternative_allele , genome_build , tissueSiteDetailId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Ieqtls — calculate_ieqtls","title":"Calculate Ieqtls — calculate_ieqtls","text":"Calculate Cell Specific eQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"calculate_ieqtls( cellType, tissueSiteDetailId, gencodeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Ieqtls — calculate_ieqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Ieqtls — calculate_ieqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Ieqtls — calculate_ieqtls","text":"","code":"# \\dontrun{ # perform request calculate_ieqtls(cellType = \"Adipocytes\", tissueSiteDetailId = \"Adipose_Subcutaneous\", gencodeId = \"ENSG00000203782.5\", variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #> cellType data datasetId enrichmentScores gencodeId genotypes regressionCoord #> #> 1 Adipocyt… gtex_v8 ENSG0000… #> # ℹ 2 more variables: tissueSiteDetailId , variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Isqtls — calculate_isqtls","title":"Calculate Isqtls — calculate_isqtls","text":"Calculate Cell Specific sQTLs. service calculates gene-variant association given pair gene variant, may may significant. requires input GENCODE ID, GTEx variant ID, tissue site detail ID. default, calculation based latest GTEx release. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"calculate_isqtls( cellType, tissueSiteDetailId, phenotypeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Isqtls — calculate_isqtls","text":"cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Isqtls — calculate_isqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Isqtls — calculate_isqtls","text":"","code":"# \\dontrun{ # perform request calculate_isqtls(cellType = \"Neutrophils\", tissueSiteDetailId = \"Whole_Blood\", phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\", variantId = \"chr1_1099341_T_C_b38\") #> # A tibble: 1 × 9 #> cellType data datasetId enrichmentScores phenotypeId tissueSiteDetailId #> #> 1 Neutrophils gtex_v8 chr1:15947:1… Whole_Blood #> # ℹ 3 more variables: variantId , genotypes , regressionCoord # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"calculate_splicing_quantitative_trait_loci( tissueSiteDetailId, phenotypeId, variantId, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. phenotypeId String. See GTEx portal FAQs details. variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/calculate_splicing_quantitative_trait_loci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Splicing Quantitative Trait Loci — calculate_splicing_quantitative_trait_loci","text":"","code":"# \\dontrun{ # perform request - returns a tibble with a single row calculate_splicing_quantitative_trait_loci( tissueSiteDetailId = \"Whole_Blood\", phenotypeId = \"chr1:15947:16607:clu_40980:ENSG00000227232.5\", variantId = \"chr1_14677_G_A_b38\") #> # A tibble: 1 × 14 #> data error genotypes hetCount homoAltCount homoRefCount maf nes #> #> 1 0.139 69 0 601 0.0515 0.757 #> # ℹ 6 more variables: pValue , pValueThreshold , phenotypeId , #> # tStatistic , tissueSiteDetailId , variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download — download","title":"Download — download","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download — download","text":"","code":"download( materialTypes = NULL, tissueSiteDetailIds = NULL, pathCategory = NULL, tissueSampleIds = NULL, sex = NULL, sortBy = NULL, sortDirection = NULL, searchTerm = NULL, sampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download — download","text":"materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download — download","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download — download","text":"Note: running request filters (.e. download()) raises error.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/download.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download — download","text":"","code":"# \\dontrun{ download( materialTypes = \"RNA:Total RNA\", tissueSiteDetailIds = \"Thyroid\", pathCategory = \"clean_specimens\", sex = \"male\", ageBrackets = \"50-59\" ) #> # A tibble: 1 × 26 #> materialType sampleId sampleIdUpper sex rin hasGTExImage concentration #> #> 1 RNA:Total RNA GTEX-WYJK-… GTEX-WYJK-16… male 7.28 TRUE 36.4 #> # ℹ 19 more variables: analysisRelease , genotype , hardyScale , #> # pathologyNotes , subjectId , tissueSiteDetailId , #> # hasGenotype , originalMaterialType , aliquotId , #> # tissueSampleId , ageBracket , brainTissueDonor , #> # volume , hasExpressionData , hasBRDImage , #> # tissueSiteDetail , pathologyNotesCategories , #> # amount , tissueSite # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Annotation — get_annotation","title":"Get Annotation — get_annotation","text":"service returns list annotations allowed values particular dataset can subsetted. Results may filtered dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Annotation — get_annotation","text":"","code":"get_annotation(datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Annotation — get_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Annotation — get_annotation","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Annotation — get_annotation","text":"Note: output function appears incomplete currently.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Annotation — get_annotation","text":"","code":"# \\dontrun{ get_annotation() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 5 #> entity values type annotation datasetId #> #> 1 subject enum sex gtex_v8 #> 2 subject enum ageBracket gtex_v8 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"Find median transcript expression data along hierarchical clusters. Returns median normalized transcript expression tissues known transcripts given gene along hierarchical clustering results tissues transcripts, based exon expression, Newick format. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"get_clustered_median_exon_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Exon Expression — get_clustered_median_exon_expression","text":"","code":"# \\dontrun{ get_clustered_median_exon_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 216 × 8 #> median exonId tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #> #> 1 0.789 ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… CRP #> 2 16.8 ENSG000… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… CRP #> 3 0.0921 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… CRP #> 4 12 ENSG000… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… CRP #> 5 1 ENSG000… Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP #> 6 22.7 ENSG000… Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP #> 7 0 ENSG000… Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP #> 8 8 ENSG000… Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP #> 9 0 ENSG000… Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP #> 10 14 ENSG000… Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP #> # ℹ 206 more rows #> # ℹ 1 more variable: unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_exon_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $exon #> [1] \"((ENSG00000203782.5_2:8.51,ENSG00000132693.12_2:8.51):0.79,(ENSG00000203782.5_1:5.92,ENSG00000132693.12_1:5.92):3.38);\" #> #> $tissue #> [1] \"(((((((((((Uterus:0.02,Stomach:0.02):0.04,(Pituitary:0.02,Brain_Cerebellum:0.02):0.04):0.01,((((Thyroid:0.03,Colon_Transverse:0.03):0.00,((Artery_Coronary:0.02,Adipose_Visceral_Omentum:0.02):0.00,(Esophagus_Muscularis:0.01,Esophagus_Gastroesophageal_Junction:0.01):0.01):0.01):0.01,Small_Intestine_Terminal_Ileum:0.04):0.00,Artery_Aorta:0.04):0.03):0.04,Kidney_Cortex:0.11):0.00,Brain_Cerebellar_Hemisphere:0.11):0.02,(((((((Ovary:0.01,Nerve_Tibial:0.01):0.00,Adipose_Subcutaneous:0.01):0.01,Esophagus_Mucosa:0.02):0.01,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.02):0.01,Minor_Salivary_Gland:0.03):0.01,(Prostate:0.02,Lung:0.02):0.02):0.04,Testis:0.09):0.04):0.02,((Fallopian_Tube:0.09,Cervix_Ectocervix:0.09):0.01,((Kidney_Medulla:0.06,Bladder:0.06):0.03,((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.04,Cervix_Endocervix:0.05):0.03):0.02):0.05):0.03,((Vagina:0.09,Brain_Hypothalamus:0.09):0.03,((((((Brain_Hippocampus:0.01,Brain_Amygdala:0.01):0.01,Cells_EBV-transformed_lymphocytes:0.02):0.01,Brain_Frontal_Cortex_BA9:0.02):0.01,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.03):0.02,(Brain_Cortex:0.02,Brain_Anterior_cingulate_cortex_BA24:0.02):0.03):0.02,(((((Brain_Substantia_nigra:0.01,Artery_Tibial:0.01):0.00,(Heart_Atrial_Appendage:0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00):0.00,Muscle_Skeletal:0.01):0.01,Colon_Sigmoid:0.02):0.01,(Whole_Blood:0.02,Heart_Left_Ventricle:0.02):0.02):0.04):0.05):0.06):0.20,Pancreas:0.39):0.34,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.71):0.12,Liver:0.85);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues along hierarchical clustering results tissues genes, based gene expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"get_clustered_median_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Gene Expression — get_clustered_median_gene_expression","text":"","code":"# \\dontrun{ get_clustered_median_gene_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 108 × 7 #> median tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 0.347 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 0.240 Adipose_Visceral_Omen… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 0.384 Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 0.198 Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 0.332 Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 0.117 Artery_Tibial UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 7 0.631 Bladder UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 8 0.0347 Brain_Amygdala UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 98 more rows # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_gene_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $gene #> [1] \"Not enough data. At least three data sets are required for clustering.\" #> #> $tissue #> [1] \"(((((((((((Cells_Cultured_fibroblasts:0.01,Bladder:0.01):0.01,Prostate:0.02):0.01,(Testis:0.02,Lung:0.02):0.02):0.01,(((((Thyroid:0.01,Minor_Salivary_Gland:0.01):0.01,Uterus:0.01):0.00,(((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.01,Small_Intestine_Terminal_Ileum:0.01):0.00,(Spleen:0.01,Breast_Mammary_Tissue:0.01):0.01):0.01):0.00,((Esophagus_Gastroesophageal_Junction:0.00,Adipose_Visceral_Omentum:0.00):0.00,Esophagus_Muscularis:0.01):0.01):0.01,((Ovary:0.00,Nerve_Tibial:0.00):0.01,Esophagus_Mucosa:0.01):0.02):0.01):0.00,(((((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.00,Colon_Transverse:0.01):0.01,Adrenal_Gland:0.02):0.00,(Kidney_Medulla:0.01,Kidney_Cortex:0.01):0.01):0.02):0.01,((((Whole_Blood:0.01,Heart_Left_Ventricle:0.01):0.01,Brain_Cerebellar_Hemisphere:0.02):0.01,(((Colon_Sigmoid:0.01,Brain_Substantia_nigra:0.01):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00,((Brain_Nucleus_accumbens_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.01):0.01):0.01):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Amygdala:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.01):0.00,Brain_Anterior_cingulate_cortex_BA24:0.01):0.00,Brain_Hippocampus:0.01):0.01,(Artery_Tibial:0.01,Artery_Aorta:0.01):0.01):0.01):0.02):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Brain_Frontal_Cortex_BA9:0.02):0.03,Vagina:0.05):0.02):0.03,((Cervix_Endocervix:0.02,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.04):0.07):0.10,Pancreas:0.20):0.37,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.07,Liver:0.64);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"Find median junction expression data along hierarchical clusters. Returns median junction read counts tissues given gene known transcripts along hierarchical clustering results tissues genes, based junction expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"get_clustered_median_junction_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Junction Expression — get_clustered_median_junction_expression","text":"","code":"# \\dontrun{ get_clustered_median_junction_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 432 × 8 #> median junctionId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 2 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 3 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 4 0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 5 0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 6 0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 7 0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 8 0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 9 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 10 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol , unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_junction_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $junction #> [1] \"((((((chr1_159713641_159714006:0.03,chr1_159713604_159714002:0.03):0.67,(chr1_159712795_159714006:0.01,chr1_159712581_159713502:0.01):0.69):0.56,chr1_159712795_159713502:1.26):0.90,chr1_159713973_159714498:2.16):0.54,chr1_159714139_159714424:2.70):2.61,chr1_153259734_153260926:5.31);\" #> #> $tissue #> [1] \"(((((((((((((((((Adipose_Visceral_Omentum:0.00,Adipose_Subcutaneous:0.00):0.00,Artery_Aorta:0.00):0.00,Artery_Coronary:0.00):0.00,Artery_Tibial:0.00):0.00,Brain_Cortex:0.00):0.00,Breast_Mammary_Tissue:0.00):0.00,Colon_Sigmoid:0.00):0.00,Heart_Atrial_Appendage:0.00):0.00,Muscle_Skeletal:0.00):0.00,Nerve_Tibial:0.00):0.00,Vagina:0.00):0.08,Kidney_Medulla:0.08):0.03,(((((((((((((((((((((Brain_Amygdala:0.00,Bladder:0.00):0.00,Brain_Anterior_cingulate_cortex_BA24:0.00):0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Cerebellar_Hemisphere:0.00):0.00,Brain_Cerebellum:0.00):0.00,Brain_Frontal_Cortex_BA9:0.00):0.00,Brain_Hippocampus:0.00):0.00,Brain_Hypothalamus:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,Brain_Putamen_basal_ganglia:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Brain_Substantia_nigra:0.00):0.00,Cells_EBV-transformed_lymphocytes:0.00):0.00,Colon_Transverse:0.00):0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Esophagus_Muscularis:0.00):0.00,Heart_Left_Ventricle:0.00):0.00,Kidney_Cortex:0.00):0.00,Pituitary:0.00):0.00,Thyroid:0.00):0.00,Whole_Blood:0.00):0.11):0.03,((((((((((((Cells_Cultured_fibroblasts:0.00,Adrenal_Gland:0.00):0.00,Esophagus_Mucosa:0.00):0.00,Fallopian_Tube:0.00):0.00,Lung:0.00):0.00,Minor_Salivary_Gland:0.00):0.00,Ovary:0.00):0.00,Prostate:0.00):0.00,Small_Intestine_Terminal_Ileum:0.00):0.00,Spleen:0.00):0.00,Stomach:0.00):0.00,Uterus:0.00):0.06,((Cervix_Endocervix:0.00,Cervix_Ectocervix:0.00):0.00,Testis:0.00):0.06):0.09):0.19,Pancreas:0.33):0.27,(Skin_Sun_Exposed_Lower_leg:0.02,Skin_Not_Sun_Exposed_Suprapubic:0.02):0.59):0.68,Liver:1.29);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"Find median transcript expression data known transcripts gene along hierarchical clusters. Returns median normalized expression tissues known transcripts given gene along hierarchical clustering results tissues genes, based expression, Newick format. Results may filtered dataset, gene tissue, least one gene must provided. hierarchical clustering performed calculating Euclidean distances using average linkage method. endpoint paginated. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"get_clustered_median_transcript_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"tibble, clustering data stored attribute, \"clusters\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_clustered_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Clustered Median Transcript Expression — get_clustered_median_transcript_expression","text":"","code":"# \\dontrun{ get_clustered_median_transcript_expression(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` #> # A tibble: 432 × 8 #> median transcriptId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0.130 ENST00000255030.9 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 2 0 ENST00000368110.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 3 0 ENST00000368111.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 4 0 ENST00000368112.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 5 0 ENST00000437342.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 6 0.0100 ENST00000473196.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 7 0 ENST00000489317.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 9 0 ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 10 0 ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 422 more rows #> # ℹ 2 more variables: geneSymbol , unit # clustering data is stored as an attribute \"clusters\" result <- get_clustered_median_transcript_expression(c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> ℹ Retrieve clustering data with `attr(, 'clusters')` attr(result, \"clusters\") #> $transcript #> [1] \"(((ENST00000473196.1:0.46,ENST00000255030.9:0.46):1.64,(((ENST00000437342.1:0.16,ENST00000368112.5:0.16):0.09,(ENST00000368111.5:0.03,ENST00000368110.1:0.03):0.21):0.15,ENST00000489317.1:0.40):1.70):2.76,ENST00000368742.3:4.86);\" #> #> $tissue #> [1] \"(((((((((((Spleen:0.00,Breast_Mammary_Tissue:0.00):0.01,Lung:0.01):0.00,((Ovary:0.01,Esophagus_Mucosa:0.01):0.00,Nerve_Tibial:0.01):0.01):0.00,((((Artery_Coronary:0.00,Adipose_Subcutaneous:0.00):0.00,Adipose_Visceral_Omentum:0.01):0.00,((Esophagus_Muscularis:0.00,Esophagus_Gastroesophageal_Junction:0.00):0.00,Thyroid:0.00):0.00):0.00,(Small_Intestine_Terminal_Ileum:0.01,Artery_Aorta:0.01):0.01):0.00):0.01,(((((Cells_EBV-transformed_lymphocytes:0.00,Brain_Hippocampus:0.00):0.00,Brain_Spinal_cord_cervical_c-1:0.00):0.00,Artery_Tibial:0.01):0.00,Brain_Amygdala:0.01):0.01,(((Brain_Putamen_basal_ganglia:0.00,Brain_Caudate_basal_ganglia:0.00):0.00,Brain_Nucleus_accumbens_basal_ganglia:0.00):0.00,((Colon_Sigmoid:0.00,Brain_Substantia_nigra:0.00):0.00,(Muscle_Skeletal:0.00,Heart_Atrial_Appendage:0.00):0.00):0.00):0.01):0.01):0.01,((((Cells_Cultured_fibroblasts:0.01,Adrenal_Gland:0.01):0.01,Kidney_Cortex:0.01):0.00,((Uterus:0.01,Prostate:0.01):0.00,Minor_Salivary_Gland:0.01):0.01):0.00,((((Heart_Left_Ventricle:0.01,Colon_Transverse:0.01):0.00,(Whole_Blood:0.00,Brain_Cerebellar_Hemisphere:0.00):0.01):0.00,((Stomach:0.00,Brain_Cerebellum:0.00):0.01,Pituitary:0.01):0.01):0.00,Kidney_Medulla:0.02):0.01):0.01):0.02,(((Brain_Hypothalamus:0.01,Brain_Cortex:0.01):0.01,Vagina:0.02):0.01,(Brain_Frontal_Cortex_BA9:0.01,Brain_Anterior_cingulate_cortex_BA24:0.01):0.02):0.03):0.01,((((Cervix_Endocervix:0.02,Bladder:0.02):0.00,Cervix_Ectocervix:0.02):0.01,Fallopian_Tube:0.03):0.02,Testis:0.05):0.01):0.15,Pancreas:0.21):0.36,(Skin_Sun_Exposed_Lower_leg:0.01,Skin_Not_Sun_Exposed_Suprapubic:0.01):0.56):0.61,Liver:1.19);\" #> # process clustering data with the ape package # install.packages(\"ape\") # phylo_tree <- ape::read.tree(text = attr(result, \"clusters\")$tissue) # plot(phylo_tree) # print(phylo_tree) # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"service returns collapsed exons gene model given gene. Gene-level exon-level expression quantification based GENCODE annotation, collapsed single transcript model gene using algorithm developed GTEx analysis team. default, service queries models used latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"get_collapsed_gene_model_exon( gencodeId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Collapsed Gene Model Exon — get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{ get_collapsed_gene_model_exon(gencodeId = \"ENSG00000132693.12\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> featureType end genomeBuild chromosome exonNumber geneSymbolUpper exonId #> #> 1 exon 159714589 GRCh38/hg38 chr1 1 CRP ENSG0… #> 2 exon 159714138 GRCh38/hg38 chr1 2 CRP ENSG0… #> # ℹ 7 more variables: datasetId , start , dataSource , #> # gencodeId , geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Dataset Info — get_dataset_info","title":"Get Dataset Info — get_dataset_info","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Dataset Info — get_dataset_info","text":"","code":"get_dataset_info(datasetId = \"gtex_v8\", organizationName = \"GTEx Consortium\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Dataset Info — get_dataset_info","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Dataset Info — get_dataset_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Dataset Info — get_dataset_info","text":"Note: current returns empty values.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_dataset_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Dataset Info — get_dataset_info","text":"","code":"# \\dontrun{ get_dataset_info() #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Downloads Page Data — get_downloads_page_data","title":"Get Downloads Page Data — get_downloads_page_data","text":"Retrieves files belonging given project_id display Downloads Page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"get_downloads_page_data(project_id = \"adult-gtex\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Downloads Page Data — get_downloads_page_data","text":"project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Downloads Page Data — get_downloads_page_data","text":"Tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Downloads Page Data — get_downloads_page_data","text":"Note: GTEx Portal API documentation states \"GTEx currently one project available: gtex\". However, project_id values \"adult-gtex\" \"egtex\" return results, whereas \"gtex\" (see examples).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_downloads_page_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Downloads Page Data — get_downloads_page_data","text":"","code":"# \\dontrun{ # \"adult-gtex\" (default `project_id` value) and \"egtex\" both return results get_downloads_page_data() #> # A tibble: 9 × 6 #> name displayName description order parent children #> #> 1 gs://adult-gtex/bulk-gex/ Bulk tissu… \"\" 1 gs://… #> 2 gs://adult-gtex/bulk-qtl/ QTL \"\" 2 gs://… #> 3 gs://adult-gtex/single-cell/ Single cell \"\" 3 gs://… #> 4 gs://adult-gtex/long-read-d… Long read … \"Long Read… 4 gs://… #> 5 gs://adult-gtex/haplotype-e… Haplotype … \"Haplotype… 5 gs://… #> 6 gs://adult-gtex/variants/ Variants \"\" 6 gs://… #> 7 gs://adult-gtex/references/ Reference \"\" 7 gs://… #> 8 gs://adult-gtex/annotations/ Metadata \"\" 8 gs://… #> 9 gs://adult-gtex/additional_… Additional… \"\" 9 gs://… egtex <- get_downloads_page_data(\"egtex\") egtex #> # A tibble: 3 × 6 #> name displayName description order parent children #> #> 1 gs://egtex/methylation/ Methylation \"\" 1 gs://… #> 2 gs://egtex/proteomics/ Proteomics \"Protein and RN… 2 gs://… #> 3 gs://egtex/telomeres/ Telomeres \"Relative telom… 3 gs://… # ...\"gtex\" does not get_downloads_page_data(\"gtex\") #> # A tibble: 0 × 0 # get details for whole blood methylation data, including download URL purrr::pluck( egtex$children, 1, \"folders\", \"Methylation - EPIC Array\", \"children\", \"folders\", \"mQTLs\", \"children\", \"files\", \"WholeBlood.mQTLs.regular.txt.gz\" ) #> $displayName #> [1] \"WholeBlood.mQTLs.regular.txt.gz\" #> #> $description #> [1] \"\" #> #> $fileSize #> [1] 43461408219 #> #> $url #> [1] \"https://storage.googleapis.com/egtex/methylation/epic-arrays/mQTLs/WholeBlood.mQTLs.regular.txt.gz\" #> #> $order #> [1] 27 #> #> $parent #> [1] \"gs://egtex/methylation/epic-arrays/mQTLs/\" #> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Eqtl Genes — get_eqtl_genes","title":"Get Eqtl Genes — get_eqtl_genes","text":"Retrieve eGenes (eQTL Genes). service returns eGenes (eQTL Genes) specified dataset. eGenes genes least one significant cis-eQTL acting upon . Results may filtered tissue. default, service queries latest GTEx release. eGene, results include allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), q-value (qValue). log2AllelicFoldChange allelic fold change (log2 scale) significant eQTL. pValue nominal p-value significant eQTL. pValueThreshold p-value threshold used determine whether cis-eQTL gene significant. details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods. empiricalPValue beta distribution-adjusted empirical p-value FastQTL. qValues calculated based empirical p-values. false discovery rate (FDR) threshold <= 0.05 applied identify genes significant eQTL. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"get_eqtl_genes( tissueSiteDetailIds, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Eqtl Genes — get_eqtl_genes","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Eqtl Genes — get_eqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_eqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Eqtl Genes — get_eqtl_genes","text":"","code":"# \\dontrun{ get_eqtl_genes(c(\"Whole_Blood\", \"Artery_Aorta\")) #> Warning: ! Total number of items (24853) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 100 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 24853 #> # A tibble: 250 × 10 #> tissueSiteDetailId ontologyId datasetId empiricalPValue gencodeId geneSymbol #> #> 1 Whole_Blood UBERON:001… gtex_v8 1.05e- 9 ENSG0000… WASH7P #> 2 Whole_Blood UBERON:001… gtex_v8 1.06e-25 ENSG0000… RP11-34P1… #> 3 Whole_Blood UBERON:001… gtex_v8 6.31e- 2 ENSG0000… CICP27 #> 4 Whole_Blood UBERON:001… gtex_v8 8.71e- 9 ENSG0000… RP11-34P1… #> 5 Whole_Blood UBERON:001… gtex_v8 6.01e-20 ENSG0000… RP11-34P1… #> 6 Whole_Blood UBERON:001… gtex_v8 6.96e- 9 ENSG0000… RP11-34P1… #> 7 Whole_Blood UBERON:001… gtex_v8 3.10e- 4 ENSG0000… RP11-34P1… #> 8 Whole_Blood UBERON:001… gtex_v8 1.92e- 3 ENSG0000… ABC7-4304… #> 9 Whole_Blood UBERON:001… gtex_v8 1.58e- 3 ENSG0000… RP11-34P1… #> 10 Whole_Blood UBERON:001… gtex_v8 7.82e- 2 ENSG0000… AP006222.2 #> # ℹ 240 more rows #> # ℹ 4 more variables: log2AllelicFoldChange , pValue , #> # pValueThreshold , qValue # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Exons — get_exons","title":"Get Exons — get_exons","text":"service returns exons known transcripts given gene. versioned GENCODE ID required ensure exons single gene. dataset ID GENCODE version genome build must provided. Although annotated exons dataset dependent, specifying dataset equivalent specifying GENCODE version genome build used dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Exons — get_exons","text":"","code":"get_exons( gencodeId, gencodeVersion = NULL, genomeBuild = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Exons — get_exons","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Exons — get_exons","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_exons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Exons — get_exons","text":"","code":"# \\dontrun{ get_exons(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #> featureType end genomeBuild start exonId source chromosome gencodeId #> #> 1 exon 153259733 GRCh38/hg38 153259700 ENSE0… HAVANA chr1 ENSG0000… #> 2 exon 153262122 GRCh38/hg38 153260927 ENSE0… HAVANA chr1 ENSG0000… #> # ℹ 5 more variables: transcriptId , geneSymbol , #> # gencodeVersion , strand , exonNumber # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Expression Pca — get_expression_pca","title":"Get Expression Pca — get_expression_pca","text":"Find gene expression PCA data. Returns gene expression PCA (principal component analysis) tissues. Results may filtered tissue, sample, dataset. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Expression Pca — get_expression_pca","text":"","code":"get_expression_pca( tissueSiteDetailIds, datasetId = \"gtex_v8\", sampleId = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Expression Pca — get_expression_pca","text":"tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Expression Pca — get_expression_pca","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_expression_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Expression Pca — get_expression_pca","text":"","code":"# \\dontrun{ get_expression_pca(tissueSiteDetailIds = c(\"Adipose_Subcutaneous\", \"Whole_Blood\")) #> Warning: ! Total number of items (1418) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1418 #> # A tibble: 250 × 7 #> pc1 pc2 pc3 sampleId tissueSiteDetailId ontologyId datasetId #> #> 1 0.0385 -0.0178 0.0769 GTEX-1117F… Adipose_Subcutane… UBERON:00… gtex_v8 #> 2 -0.0585 0.00809 0.00492 GTEX-111CU… Adipose_Subcutane… UBERON:00… gtex_v8 #> 3 0.140 -0.0308 -0.0368 GTEX-111FC… Adipose_Subcutane… UBERON:00… gtex_v8 #> 4 0.0597 0.140 0.0294 GTEX-111VG… Adipose_Subcutane… UBERON:00… gtex_v8 #> 5 -0.0968 0.00233 -0.0174 GTEX-111YS… Adipose_Subcutane… UBERON:00… gtex_v8 #> 6 -0.120 0.0195 -0.0594 GTEX-1122O… Adipose_Subcutane… UBERON:00… gtex_v8 #> 7 -0.102 0.0652 0.00344 GTEX-1128S… Adipose_Subcutane… UBERON:00… gtex_v8 #> 8 0.105 0.0174 -0.0568 GTEX-113IC… Adipose_Subcutane… UBERON:00… gtex_v8 #> 9 -0.109 -0.0543 0.00594 GTEX-117YX… Adipose_Subcutane… UBERON:00… gtex_v8 #> 10 0.132 -0.0335 -0.0350 GTEX-11DXW… Adipose_Subcutane… UBERON:00… gtex_v8 #> # ℹ 240 more rows get_expression_pca(tissueSiteDetailIds = \"Adipose_Subcutaneous\", sampleId = \"GTEX-1117F-0226-SM-5GZZ7\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 7 #> pc1 pc2 pc3 sampleId tissueSiteDetailId ontologyId datasetId #> #> 1 0.0385 -0.0178 0.0769 GTEX-1117F-0226… Adipose_Subcutane… UBERON:00… gtex_v8 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Get File List — get_file_list","title":"Get File List — get_file_list","text":"Get files GTEx dataset Download page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get File List — get_file_list","text":"","code":"get_file_list()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get File List — get_file_list","text":"tibble","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get File List — get_file_list","text":"returned tibble includes nested list column, \"filesets\". details files, sub-categorised fileset (see examples section).","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_file_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get File List — get_file_list","text":"","code":"# \\dontrun{ # Column \"filesets\" is a list column get_file_list() #> # A tibble: 11 × 10 #> name subpath dbgapId dataset release order type id description #> #> 1 GTEx Analysis … gtex_a… \"phs00… GTEx v3 10 data… gtex… \"\" #> 2 GTEx Analysis … gtex_a… \"\" GTEx v6p 7 data… gtex… \"The GTEx … #> 3 Biobank Invent… gtex_b… \"\" GTEx biobank 5 data… biob… \"\" #> 4 GTEx Analysis … gtex_a… \"phs00… GTEx v7 6 data… gtex… \"\" #> 5 GTEx Analysis … gtex_a… \"phs00… GTEx v6 8 data… gtex… \"\" #> 6 Additional Dat… gtex_a… \"\" GTEx additi… 3 data… addi… \"\" #> 7 GTEx Analysis … gtex_a… \"phs00… GTEx v4 9 data… gtex… \"\" #> 8 External Datas… gtex_e… \"\" GTEx extern… 4 data… exte… \"\" #> 9 GTEx Analysis … gtex_a… \"phs00… GTEx v8 1 data… gtex… \"The GTEx … #> 10 eGTEx gtex_e… \"\" GTEx egtex 2 data… egtex \"The Enhan… #> 11 GTEx Analysis … gtex_a… \"phs00… GTEx v9 0 data… gtex… \"Open-acce… #> # ℹ 1 more variable: filesets # Get \"GTEx Analysis V9\" file list gtex_v9_files <- get_file_list() |> dplyr::filter(name == \"GTEx Analysis V9\") |> dplyr::pull(filesets) # \"GTEx Analysis V9\" filesets names(gtex_v9_files[[1]]) #> [1] \"snRNA-Seq Data\" \"Long Read Data\" # \"GTEx Analysis V9\", \"snRNA-Seq Data\" fileset files names(gtex_v9_files[[1]][[\"snRNA-Seq Data\"]]$files) #> [1] \"GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad\" #> [2] \"GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad\" # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Fine Mapping — get_fine_mapping","title":"Get Fine Mapping — get_fine_mapping","text":"Retrieve Fine Mapping Data Finds returns Fine Mapping data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"get_fine_mapping( gencodeIds, datasetId = \"gtex_v8\", variantId = NULL, tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Fine Mapping — get_fine_mapping","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". variantId String. gtex variant ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Fine Mapping — get_fine_mapping","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_fine_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Fine Mapping — get_fine_mapping","text":"","code":"# \\dontrun{ # search by gene get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 27 #> # A tibble: 27 × 9 #> datasetId gencodeId method pip setId setSize tissueSiteDetailId #> #> 1 gtex_v8 ENSG00000132693.12 DAP-G 0.0235 1 5 Thyroid #> 2 gtex_v8 ENSG00000132693.12 DAP-G 0.0221 1 5 Thyroid #> 3 gtex_v8 ENSG00000132693.12 DAP-G 0.0171 1 5 Thyroid #> 4 gtex_v8 ENSG00000132693.12 DAP-G 0.0252 1 5 Thyroid #> 5 gtex_v8 ENSG00000132693.12 DAP-G 0.892 1 5 Thyroid #> 6 gtex_v8 ENSG00000203782.5 DAP-G 0.0126 1 22 Whole_Blood #> 7 gtex_v8 ENSG00000203782.5 DAP-G 0.00690 1 22 Whole_Blood #> 8 gtex_v8 ENSG00000203782.5 DAP-G 0.0313 1 22 Whole_Blood #> 9 gtex_v8 ENSG00000203782.5 DAP-G 0.00852 1 22 Whole_Blood #> 10 gtex_v8 ENSG00000203782.5 DAP-G 0.0105 1 22 Whole_Blood #> # ℹ 17 more rows #> # ℹ 2 more variables: ontologyId , variantId # optionally filter for a single variant and/or one or more tissues get_fine_mapping(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), variantId = \"chr1_153228363_A_G_b38\", tissueSiteDetailIds = c(\"Whole_Blood\", \"Thyroid\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 9 #> datasetId gencodeId method pip setId setSize tissueSiteDetailId ontologyId #> #> 1 gtex_v8 ENSG00000… DAP-G 0.0126 1 22 Whole_Blood UBERON:00… #> # ℹ 1 more variable: variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"service allows user query full Collapsed Gene Model Exon specific gene gencode ID GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"get_full_get_collapsed_gene_model_exon(gencodeId, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_full_get_collapsed_gene_model_exon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Full Get Collapsed Gene Model Exon — get_full_get_collapsed_gene_model_exon","text":"","code":"# \\dontrun{ get_full_get_collapsed_gene_model_exon(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> featureType end genomeBuild chromosome exonNumber geneSymbolUpper exonId #> #> 1 exon 153259733 GRCh38/hg38 chr1 1 LOR ENSG0… #> 2 exon 153262122 GRCh38/hg38 chr1 2 LOR ENSG0… #> # ℹ 7 more variables: datasetId , start , dataSource , #> # gencodeId , geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Functional Annotation — get_functional_annotation","title":"Get Functional Annotation — get_functional_annotation","text":"endpoint retrieves functional annotation certain chromosome location. Default recent dataset release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"get_functional_annotation( datasetId = \"gtex_v8\", chromosome, start, end, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Functional Annotation — get_functional_annotation","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". start Integer. end Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Functional Annotation — get_functional_annotation","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_functional_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Functional Annotation — get_functional_annotation","text":"","code":"# \\dontrun{ get_functional_annotation(chromosome = \"chr1\", start = 192168000, end = 192169000) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3 #> # A tibble: 3 × 23 #> variantId enhancer promoter openChromatinRegion promoterFlankingRegion #> #> 1 chr1_192168015_T… TRUE FALSE FALSE FALSE #> 2 chr1_192168266_T… TRUE FALSE FALSE FALSE #> 3 chr1_192168728_T… FALSE FALSE FALSE FALSE #> # ℹ 18 more variables: ctcfBindingSite , tfBindingSite , #> # `3PrimeUtrVariant` , `5PrimeUtrVariant` , #> # frameshiftVariant , intronVariant , missenseVariant , #> # nonCodingTranscriptExonVariant , spliceAcceptorVariant , #> # spliceDonorVariant , spliceRegionVariant , stopGained , #> # synonymousVariant , chromosome , pos , ref , alt , #> # datasetId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Expression — get_gene_expression","title":"Get Gene Expression — get_gene_expression","text":"Find normalized gene expression data. Returns normalized gene expression tissues sample level. Results may filtered dataset, gene tissue, least one gene must provided. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Expression — get_gene_expression","text":"","code":"get_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, attributeSubset = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Expression — get_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Expression — get_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Expression — get_gene_expression","text":"","code":"# \\dontrun{ # multiple genes, selected tissues get_gene_expression(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), tissueSiteDetailIds = c(\"Thyroid\", \"Whole_Blood\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Thyroid UBERON:00… gtex_v8 ENSG0000… LOR TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… LOR TPM #> 3 Thyroid UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # single gene, selected (single) tissue get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # subset by sex get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\", attributeSubset = \"sex\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 2 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # subset by age bracket get_gene_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\", attributeSubset = \"ageBracket\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 6 × 8 #> data tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 1 more variable: subsetGroup # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gene Search — get_gene_search","title":"Get Gene Search — get_gene_search","text":"Find genes partial complete match gene_id gene_id gene symbol, gencode ID, Ensemble ID Gencode Version Genome Build must specified GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gene Search — get_gene_search","text":"","code":"get_gene_search( geneId, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gene Search — get_gene_search","text":"geneId String. gene symbol, gencode ID, Ensemble ID. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gene Search — get_gene_search","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gene_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gene Search — get_gene_search","text":"","code":"# \\dontrun{ get_gene_search(\"CRP\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #> chromosome dataSource description end gencodeId gencodeVersion geneStatus #> #> 1 chr1 HAVANA C-reactive p… 1.60e8 ENSG0000… v26 \"\" #> 2 chr1 HAVANA C-reactive p… 1.60e8 ENSG0000… v26 \"\" #> # ℹ 8 more variables: geneSymbol , geneSymbolUpper , geneType , #> # genomeBuild , start , strand , tss , entrezGeneId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genes — get_genes","title":"Get Genes — get_genes","text":"service returns information reference genes. genome build GENCODE version must provided. Genes searchable gene symbol, GENCODE ID versioned GENCODE ID. Versioned GENCODE ID recommended ensure unique ID matching. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genes — get_genes","text":"","code":"get_genes( geneIds, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genes — get_genes","text":"geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genes — get_genes","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genes — get_genes","text":"","code":"# \\dontrun{ get_genes(c(\"CRP\", \"IL6R\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 15 #> chromosome dataSource description end entrezGeneId gencodeId gencodeVersion #> #> 1 chr1 HAVANA interleuki… 1.54e8 3570 ENSG0000… v26 #> 2 chr1 HAVANA C-reactive… 1.60e8 1401 ENSG0000… v26 #> # ℹ 8 more variables: geneStatus , geneSymbol , #> # geneSymbolUpper , geneType , genomeBuild , start , #> # strand , tss # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Genomic Features — get_genomic_features","title":"Get Genomic Features — get_genomic_features","text":"GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Genomic Features — get_genomic_features","text":"","code":"get_genomic_features(.featureId, datasetId = \"gtex_v8\")"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Genomic Features — get_genomic_features","text":".featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Genomic Features — get_genomic_features","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Genomic Features — get_genomic_features","text":"endpoint takes path parameter \"featureId\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_genomic_features.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Genomic Features — get_genomic_features","text":"","code":"# \\dontrun{ # gene symbol get_genomic_features(\"brca1\") #> # A tibble: 1 × 17 #> gencodeVersion end description geneSymbolUpper genomeBuild geneStatus #> #> 1 v26 43170245 BRCA1, DNA rep… BRCA1 GRCh38/hg38 \"\" #> # ℹ 11 more variables: strand , entrezGeneId , geneType , #> # start , dataSource , gencodeId , geneSymbol , #> # tss , chromosome , featureType , assembly # GENCODE ID get_genomic_features(\"ENSG00000132693.12\") #> # A tibble: 1 × 17 #> gencodeVersion end description geneSymbolUpper genomeBuild geneStatus #> #> 1 v26 159714589 C-reactive pr… CRP GRCh38/hg38 \"\" #> # ℹ 11 more variables: strand , entrezGeneId , geneType , #> # start , dataSource , gencodeId , geneSymbol , #> # tss , chromosome , featureType , assembly # RSID get_genomic_features(\"rs1815739\") #> # A tibble: 1 × 8 #> featureType chromosome start snpId variantId ref alt assembly #> #> 1 snp chr11 66560624 rs1815739 chr11_66560624… C T HG38 # GTEx variant ID get_genomic_features(\"chr11_66561023_G_GTTA_b38\") #> # A tibble: 1 × 8 #> featureType chromosome start snpId variantId ref alt assembly #> #> 1 snp chr11 66561023 rs3837428 chr11_66561023… G GTTA HG38 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"Find GWAS Catalog certain chromosome start end locations. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"get_gwas_catalog_by_location( start, end, chromosome, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_gwas_catalog_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Gwas Catalog By Location — get_gwas_catalog_by_location","text":"","code":"# \\dontrun{ get_gwas_catalog_by_location(start = 1, end = 10000000, chromosome = \"chr1\") #> Warning: ! Total number of items (316) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 316 #> # A tibble: 250 × 10 #> chromosome start end phenotype pValue beta pubmedId snpId riskAllele #> #> 1 chr1 9653328 9653329 Testicula… 6e-13 1.14 28604728 rs42… T #> 2 chr1 8428505 8428506 Autism sp… 7e- 9 1.06 28540026 rs30… ? #> 3 chr1 9651584 9651585 Monocyte … 2e- 9 0.0222 27863252 rs75… G #> 4 chr1 3080038 3080039 Mean corp… 1e-13 0.0311 27863252 rs15… C #> 5 chr1 3811497 3811498 Mean corp… 1e-13 0.0301 27863252 rs12… T #> 6 chr1 4544044 4544045 Adolescen… 3e- 9 1.2 26394188 rs24… ? #> 7 chr1 1312114 1312115 Inflammat… 8e-13 1.10 23128233 rs12… A #> 8 chr1 7961913 7961914 Inflammat… 1e-15 1.11 23128233 rs35… G #> 9 chr1 8444361 8444362 Eosinophi… 2e-19 0.0328 27863252 rs15… A #> 10 chr1 9281727 9281728 Eosinophi… 1e-10 0.0260 27863252 rs67… T #> # ℹ 240 more rows #> # ℹ 1 more variable: genomeBuild # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Image — get_image","title":"Get Image — get_image","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Image — get_image","text":"","code":"get_image(tissueSampleIds = NULL, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Image — get_image","text":"tissueSampleIds Array strings. list Tissue Sample ID(s). page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Image — get_image","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_image.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Image — get_image","text":"","code":"# \\dontrun{ get_image() #> Warning: ! Total number of items (25713) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 103 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25713 #> # A tibble: 250 × 11 #> ageBracket hardyScale hide histologyImageId pathologyNotes sex subjectId #> #> 1 60-69 Slow death FALSE GTEX-1117F-0126 6 pieces, minim… fema… GTEX-111… #> 2 60-69 Slow death FALSE GTEX-1117F-0226 2 pieces, ~15% … fema… GTEX-111… #> 3 60-69 Slow death FALSE GTEX-1117F-0326 2 pieces, clean… fema… GTEX-111… #> 4 60-69 Slow death FALSE GTEX-1117F-0426 2 pieces, !5% f… fema… GTEX-111… #> 5 60-69 Slow death FALSE GTEX-1117F-0526 2 pieces, clean… fema… GTEX-111… #> 6 60-69 Slow death FALSE GTEX-1117F-0626 2 pieces, up to… fema… GTEX-111… #> 7 60-69 Slow death FALSE GTEX-1117F-0726 2 pieces, no ab… fema… GTEX-111… #> 8 60-69 Slow death FALSE GTEX-1117F-0826 2 pieces, exten… fema… GTEX-111… #> 9 60-69 Slow death FALSE GTEX-1117F-0926 6 pieces, adher… fema… GTEX-111… #> 10 60-69 Slow death FALSE GTEX-1117F-1026 2 pieces, moder… fema… GTEX-111… #> # ℹ 240 more rows #> # ℹ 4 more variables: tissueSiteDetail , sampleId , #> # tissueSampleId , pathologyNotesCategories # filter by `tissueSampleId` result <- get_image(tissueSampleIds = \"GTEX-1117F-0526\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 print(result) #> # A tibble: 1 × 11 #> ageBracket hardyScale hide histologyImageId pathologyNotes #> #> 1 60-69 Slow death FALSE GTEX-1117F-0526 2 pieces, clean, Monckebeg media… #> # ℹ 6 more variables: pathologyNotesCategories , sampleId , #> # sex , subjectId , tissueSampleId , tissueSiteDetail # note that `pathologyNotesCategories` (if present) is a list column print(result$pathologyNotesCategories) #> # A tibble: 1 × 2 #> monckeberg sclerotic #> #> 1 TRUE TRUE # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Independent Eqtl — get_independent_eqtl","title":"Get Independent Eqtl — get_independent_eqtl","text":"Retrieve Independent eQTL Data Finds returns Independent eQTL Data data provided list genes default, endpoint fetches data latest GTEx version retrieved data split pages items_per_page entries per page GTEx portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"get_independent_eqtl( gencodeIds, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Independent Eqtl — get_independent_eqtl","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Independent Eqtl — get_independent_eqtl","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_independent_eqtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Independent Eqtl — get_independent_eqtl","text":"","code":"# \\dontrun{ # search by gene get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 8 #> # A tibble: 8 × 14 #> gencodeId geneSymbol variantId snpId tissueSiteDetailId ontologyId rank #> #> 1 ENSG0000013269… CRP chr1_160… rs66… Esophagus_Gastroe… UBERON:00… 1 #> 2 ENSG0000013269… CRP chr1_159… rs57… Thyroid UBERON:00… 1 #> 3 ENSG0000020378… LOR chr1_153… rs14… Artery_Coronary UBERON:00… 1 #> 4 ENSG0000020378… LOR chr1_153… rs87… Whole_Blood UBERON:00… 1 #> 5 ENSG0000020378… LOR chr1_153… rs12… Skin_Sun_Exposed_… UBERON:00… 1 #> 6 ENSG0000020378… LOR chr1_152… rs77… Heart_Atrial_Appe… UBERON:00… 1 #> 7 ENSG0000020378… LOR chr1_153… rs12… Esophagus_Mucosa UBERON:00… 1 #> 8 ENSG0000013269… CRP chr1_159… rs86… Muscle_Skeletal UBERON:00… 1 #> # ℹ 7 more variables: tssDistance , maf , pValue , nes , #> # chromosome , pos , datasetId # optionally filter for a single variant and/or one or more tissues get_independent_eqtl(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), tissueSiteDetailIds = c(\"Whole_Blood\", \"Thyroid\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 14 #> gencodeId geneSymbol variantId snpId tissueSiteDetailId ontologyId rank #> #> 1 ENSG0000013269… CRP chr1_159… rs57… Thyroid UBERON:00… 1 #> 2 ENSG0000020378… LOR chr1_153… rs87… Whole_Blood UBERON:00… 1 #> # ℹ 7 more variables: tssDistance , maf , pValue , nes , #> # chromosome , pos , datasetId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"Find linkage disequilibrium (LD) data given variant GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data( variantId, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"variantId String. gtex variant ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_by_variant_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium By Variant Data — get_linkage_disequilibrium_by_variant_data","text":"","code":"get_linkage_disequilibrium_by_variant_data(\"chr1_159245536_C_T_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 241 #> # A tibble: 241 × 3 #> variantId_1 variantId_2 ld #> #> 1 chr1_159163610_GA_G_b38 chr1_159245536_C_T_b38 0.114 #> 2 chr1_159163924_G_A_b38 chr1_159245536_C_T_b38 0.114 #> 3 chr1_159164864_T_C_b38 chr1_159245536_C_T_b38 0.114 #> 4 chr1_159165054_A_G_b38 chr1_159245536_C_T_b38 0.113 #> 5 chr1_159165563_T_C_b38 chr1_159245536_C_T_b38 0.113 #> 6 chr1_159174791_T_C_b38 chr1_159245536_C_T_b38 0.252 #> 7 chr1_159176518_G_T_b38 chr1_159245536_C_T_b38 0.146 #> 8 chr1_159176900_C_A_b38 chr1_159245536_C_T_b38 0.271 #> 9 chr1_159177147_A_T_b38 chr1_159245536_C_T_b38 0.274 #> 10 chr1_159179691_T_C_b38 chr1_159245536_C_T_b38 0.253 #> # ℹ 231 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"Find linkage disequilibrium (LD) data given gene. endpoint returns linkage disequilibrium data cis-eQTLs found associated provided gene specified dataset. Results queried gencode ID. default, service queries latest GTEx release. Specify dataset ID fetch results different dataset. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data( gencodeId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_linkage_disequilibrium_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Linkage Disequilibrium Data — get_linkage_disequilibrium_data","text":"","code":"get_linkage_disequilibrium_data(gencodeId = \"ENSG00000132693.12\") #> Warning: ! Total number of items (3558) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 15 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3558 #> # A tibble: 250 × 3 #> variantId_1 variantId_2 ld #> #> 1 chr1_159230230_G_T_b38 chr1_159230339_A_C_b38 1 #> 2 chr1_159230230_G_T_b38 chr1_159245536_C_T_b38 0.971 #> 3 chr1_159230230_G_T_b38 chr1_159302270_T_C_b38 0.717 #> 4 chr1_159230230_G_T_b38 chr1_159343657_A_T_b38 0.302 #> 5 chr1_159230230_G_T_b38 chr1_159344052_G_A_b38 0.300 #> 6 chr1_159230230_G_T_b38 chr1_159347493_G_A_b38 0.300 #> 7 chr1_159230230_G_T_b38 chr1_159350390_C_A_b38 0.300 #> 8 chr1_159230230_G_T_b38 chr1_159351189_G_A_b38 0.300 #> 9 chr1_159230230_G_T_b38 chr1_159359256_C_A_b38 0.302 #> 10 chr1_159230230_G_T_b38 chr1_159360755_ATACATAAGTG_A_b38 0.300 #> # ℹ 240 more rows"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Maintenance Message — get_maintenance_message","title":"Get Maintenance Message — get_maintenance_message","text":"Getting maintenance messages database enabled. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"get_maintenance_message(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Maintenance Message — get_maintenance_message","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Maintenance Message — get_maintenance_message","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Maintenance Message — get_maintenance_message","text":"Note typically returns empty tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_maintenance_message.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Maintenance Message — get_maintenance_message","text":"","code":"# \\dontrun{ get_maintenance_message() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 0 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 0 #> # A tibble: 0 × 0 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Exon Expression — get_median_exon_expression","title":"Get Median Exon Expression — get_median_exon_expression","text":"Find median exon expression data. Returns median exon read counts, tissues, collapsed gene model. Results may filtered dataset, gene tissue, least one gene must provided default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"get_median_exon_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Exon Expression — get_median_exon_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Exon Expression — get_median_exon_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_exon_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Exon Expression — get_median_exon_expression","text":"","code":"# \\dontrun{ # median exon expression values for CRP, filtered for whole blood get_median_exon_expression(gencodeIds = \"ENSG00000132693.12\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 8 #> median exonId tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol #> #> 1 0 ENSG00000… Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP #> 2 5 ENSG00000… Whole_Blood UBERON:00… gtex_v8 ENSG0000… CRP #> # ℹ 1 more variable: unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Gene Expression — get_median_gene_expression","title":"Get Median Gene Expression — get_median_gene_expression","text":"Find median gene expression data along hierarchical clusters. Returns median gene expression tissues. default, endpoint queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"get_median_gene_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Gene Expression — get_median_gene_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Gene Expression — get_median_gene_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_gene_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Gene Expression — get_median_gene_expression","text":"","code":"# \\dontrun{ get_median_gene_expression(gencodeIds = \"ENSG00000132693.12\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 7 #> median tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol unit #> #> 1 0.347 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 2 0.240 Adipose_Visceral_Omen… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 3 0.384 Adrenal_Gland UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 4 0.198 Artery_Aorta UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 5 0.332 Artery_Coronary UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 6 0.117 Artery_Tibial UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 7 0.631 Bladder UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 8 0.0347 Brain_Amygdala UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8 ENSG0000… CRP TPM #> # ℹ 44 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Junction Expression — get_median_junction_expression","title":"Get Median Junction Expression — get_median_junction_expression","text":"Find junction gene expression data. Returns median junction read counts tissues given gene known transcripts. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"get_median_junction_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Junction Expression — get_median_junction_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Junction Expression — get_median_junction_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_junction_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Junction Expression — get_median_junction_expression","text":"","code":"# \\dontrun{ get_median_junction_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #> median junctionId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0 chr1_159712581_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 2 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 3 0 chr1_159712795_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 4 0 chr1_159713604_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 5 0 chr1_159713641_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 6 0 chr1_159713973_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 7 0 chr1_159714139_1597… Adipose_Subcutane… UBERON:00… gtex_v8 ENSG0000… #> 8 0 chr1_159712581_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 9 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> 10 0 chr1_159712795_1597… Adipose_Visceral_… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol , unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Median Transcript Expression — get_median_transcript_expression","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"Find median transcript expression data known transcripts gene. Returns median normalized expression tissues known transcripts given gene. Results may filtered dataset tissue. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"get_median_transcript_expression( gencodeIds, datasetId = \"gtex_v8\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_median_transcript_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Median Transcript Expression — get_median_transcript_expression","text":"","code":"# \\dontrun{ get_median_transcript_expression(gencodeIds = \"ENSG00000132693.12\") #> Warning: ! Total number of items (378) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 2 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 378 #> # A tibble: 250 × 8 #> median transcriptId tissueSiteDetailId ontologyId datasetId gencodeId #> #> 1 0.130 ENST00000255030.9 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 2 0 ENST00000368110.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 3 0 ENST00000368111.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 4 0 ENST00000368112.5 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 5 0 ENST00000437342.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 6 0.0100 ENST00000473196.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 7 0 ENST00000489317.1 Adipose_Subcutaneous UBERON:00… gtex_v8 ENSG0000… #> 8 0.0900 ENST00000255030.9 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 9 0 ENST00000368110.1 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> 10 0 ENST00000368111.5 Adipose_Visceral_Ome… UBERON:00… gtex_v8 ENSG0000… #> # ℹ 240 more rows #> # ℹ 2 more variables: geneSymbol , unit # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"Find multi-tissue eQTL Metasoft results. service returns multi-tissue eQTL Metasoft results given gene variant specified dataset. Versioned GENCODE ID must provided. tissue, results include: m-value (mValue), normalized effect size (nes), p-value (pValue), standard error (se). m-value posterior probability eQTL effect exists tissue tested cross-tissue meta-analysis (Han Eskin, PLoS Genetics 8(3): e1002555, 2012). normalized effect size slope linear regression normalized expression data versus three genotype categories using single-tissue eQTL analysis, representing eQTL effect size. p-value t-test compares observed NES single-tissue eQTL analysis null NES 0. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"get_multi_tissue_eqtls( gencodeIds, variantId = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantId String. gtex variant ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_multi_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Multi Tissue Eqtls — get_multi_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_multi_tissue_eqtls(gencodeId = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 132 #> # A tibble: 6,468 × 5 #> gencodeId datasetId metaP variantId tissues #> #> 1 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 2 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 3 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 4 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 5 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 6 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 7 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 8 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 9 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> 10 ENSG00000203782.5 gtex_v8 0.00177 chr1_152346526_G_T_b38 #> # ℹ 6,458 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Neighbor Gene — get_neighbor_gene","title":"Get Neighbor Gene — get_neighbor_gene","text":"Find neighboring genes certain chromosome around position certain window size. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"get_neighbor_gene(pos, chromosome, bp_window, page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Neighbor Gene — get_neighbor_gene","text":"pos Integer, vector. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". bp_window Integer. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Neighbor Gene — get_neighbor_gene","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_neighbor_gene.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Neighbor Gene — get_neighbor_gene","text":"","code":"# \\dontrun{ get_neighbor_gene(pos = 1000000, chromosome = \"chr1\", bp_window = 10000) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 15 #> chromosome dataSource description end gencodeId gencodeVersion geneStatus #> #> 1 chr1 HAVANA novel transc… 9.98e5 ENSG0000… v26 \"\" #> 2 chr1 HAVANA hes family b… 1.00e6 ENSG0000… v26 \"\" #> 3 chr1 HAVANA ISG15 ubiqui… 1.01e6 ENSG0000… v26 \"\" #> 4 chr1 HAVANA ribosomal pr… 1.01e6 ENSG0000… v26 \"\" #> # ℹ 8 more variables: geneSymbol , geneSymbolUpper , geneType , #> # genomeBuild , start , strand , tss , entrezGeneId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":null,"dir":"Reference","previous_headings":"","what":"Get News Item — get_news_item","title":"Get News Item — get_news_item","text":"Getting news items database current. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get News Item — get_news_item","text":"","code":"get_news_item(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get News Item — get_news_item","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get News Item — get_news_item","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_news_item.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get News Item — get_news_item","text":"","code":"# \\dontrun{ get_news_item() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 23 #> # A tibble: 23 × 6 #> title newsText rank dateCreated release id #> #> 1 New Top 50 Expressed Genes Visualiz… \"The GT… 240 2018-04-04 news_i… 240 #> 2 New Multi-Gene Query Visualization \"The GT… 250 2018-04-04 news_i… 250 #> 3 New eQTL Dashboard Visualization \"The GT… 260 2018-04-04 news_i… 260 #> 4 Video Tutorial for the Gene-eQTL Vi… \"Watch … 270 2018-04-05 news_i… 270 #> 5 Access GTEx Biospecimens Here \"We hav… 280 2018-05-10 news_i… 280 #> 6 Access GTEx Data Programmatically w… \"You ca… 290 2018-09-20 news_i… 290 #> 7 Reuse GTEx Visualizations On Your W… \"You ca… 300 2018-09-20 news_i… 300 #> 8 Use The GTEx Portal On Your Phone \"We hav… 310 2018-09-20 news_i… 310 #> 9 GTEx Portal Visualizations Updated \"We hav… 320 2018-12-06 news_i… 320 #> 10 Help Us Help You: New Feature Survey \"PLEASE… 331 2019-02-06 news_i… 331 #> # ℹ 13 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Biobank Data) — get_sample_biobank_data","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"get_sample_biobank_data( draw = NULL, materialTypes = NULL, tissueSiteDetailIds = NULL, pathCategory = NULL, tissueSampleIds = NULL, sex = NULL, sortBy = \"sampleId\", sortDirection = \"asc\", searchTerm = NULL, sampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"draw Integer. materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSampleIds Array strings. list Tissue Sample ID(s). sex String. Options: \"male\", \"female\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". searchTerm String. sampleIds Character vector. GTEx sample ID. subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_biobank_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Biobank Data) — get_sample_biobank_data","text":"","code":"# \\dontrun{ get_sample_biobank_data(tissueSiteDetailIds = \"Whole_Blood\") #> Warning: ! Total number of items (1329) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 6 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems (recordsFiltered) = 1329 #> • recordsTotal = 72513 #> # A tibble: 250 × 26 #> materialType sampleId sampleIdUpper sex hasGTExImage concentration #> #> 1 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 190. #> 2 RNA:Total RNA GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 154 #> 3 RNA:Total RNA GTEX-1117F-00… GTEX-1117F-0… fema… FALSE 41.2 #> 4 DNA:DNA Genomic GTEX-111CU-00… GTEX-111CU-0… male FALSE 85.9 #> 5 RNA:Total RNA GTEX-111CU-00… GTEX-111CU-0… male FALSE 96.0 #> 6 RNA:Total RNA GTEX-111CU-00… GTEX-111CU-0… male FALSE 95.3 #> 7 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male FALSE 142. #> 8 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male FALSE 4.35 #> 9 RNA:Total RNA GTEX-111FC-00… GTEX-111FC-0… male FALSE 128. #> 10 RNA:Total RNA GTEX-111FC-00… GTEX-111FC-0… male FALSE 128. #> # ℹ 240 more rows #> # ℹ 20 more variables: analysisRelease , genotype , hardyScale , #> # pathologyNotes , subjectId , tissueSiteDetailId , #> # hasGenotype , originalMaterialType , aliquotId , #> # tissueSampleId , ageBracket , brainTissueDonor , #> # volume , hasExpressionData , hasBRDImage , #> # tissueSiteDetail , amount , mass , tissueSite , … # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"service returns information samples used analyses datasets. Results may filtered dataset ID, sample ID, subject ID, sample metadata, provided parameters. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"get_sample_datasets_endpoints( datasetId = \"gtex_v8\", sampleIds = NULL, tissueSampleIds = NULL, subjectIds = NULL, ageBrackets = NULL, sex = NULL, pathCategory = NULL, tissueSiteDetailId = NULL, aliquotIds = NULL, autolysisScores = NULL, hardyScales = NULL, ischemicTime = NULL, ischemicTimeGroups = NULL, rin = NULL, uberonIds = NULL, dataTypes = NULL, sortBy = NULL, sortDirection = NULL, page = NULL, itemsPerPage = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sampleIds Character vector. GTEx sample ID. tissueSampleIds Array strings. list Tissue Sample ID(s). subjectIds Character vector. GTEx subject ID. ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". sex String. Options: \"male\", \"female\". pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. aliquotIds Character vector. autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". rin Integer vector. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sample_datasets_endpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sample (Datasets Endpoints) — get_sample_datasets_endpoints","text":"","code":"# \\dontrun{ get_sample_datasets_endpoints() #> Warning: ! Total number of items (22734) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 91 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 22734 #> # A tibble: 10,946 × 20 #> ischemicTime aliquotId tissueSampleId tissueSiteDetail dataType #> #> 1 1188 SM-58Q7G GTEX-1117F-0003 Whole Blood WES #> 2 1188 SM-5DWSB GTEX-1117F-0003 Whole Blood OMNI #> 3 1188 SM-6WBT7 GTEX-1117F-0003 Whole Blood WGS #> 4 1193 SM-AHZ7F GTEX-1117F-0011-R10a Brain - Frontal Cortex … NA #> 5 1193 SM-CYKQ8 GTEX-1117F-0011-R10b Brain - Frontal Cortex … NA #> 6 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 7 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 8 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 9 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> 10 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ #> # ℹ 10,936 more rows #> # ℹ 15 more variables: ischemicTimeGroup , freezeType , #> # sampleId , sampleIdUpper , ageBracket , hardyScale , #> # tissueSiteDetailId , subjectId , uberonId , sex , #> # datasetId , rin , pathologyNotesCategories , #> # pathologyNotes , autolysisScore # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Service Info — get_service_info","title":"Get Service Info — get_service_info","text":"General information GTEx service. GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Service Info — get_service_info","text":"","code":"get_service_info()"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Service Info — get_service_info","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_service_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Service Info — get_service_info","text":"","code":"# \\dontrun{ get_service_info() #> # A tibble: 1 × 9 #> id name version organization_name organization_url description contactUrl #> #> 1 org.g… GTEx… 2.0.0 GTEx Project https://gtexpor… This servi… https://g… #> # ℹ 2 more variables: documentationUrl , environment # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Find significant single tissue eQTLs. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, gene, variant dataset. search gene, use versioned GENCODE ID. search variant, use dbSNP rs ID (snpId). default, service queries latest GTEx release retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"get_significant_single_tissue_eqtls( gencodeIds = NULL, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"tibble.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"Note: although GTEx Portal API documentation says use dbSNP rsID searching variant, returns results. Instead use gtex variant IDs e.g. use \"chr1_153209640_C_A_b38\" instead \"rs1410858\".","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Eqtls — get_significant_single_tissue_eqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 249 #> # A tibble: 249 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs12128960 159343657 RS12128960 chr1_1593… CRP 8.52e-5 CRP #> 2 rs12132451 159344052 RS12132451 chr1_1593… CRP 7.92e-5 CRP #> 3 rs12136402 159347493 RS12136402 chr1_1593… CRP 7.92e-5 CRP #> 4 rs10908709 159350390 RS10908709 chr1_1593… CRP 7.92e-5 CRP #> 5 rs10908710 159351189 RS10908710 chr1_1593… CRP 7.92e-5 CRP #> 6 rs11265178 159359256 RS11265178 chr1_1593… CRP 9.62e-5 CRP #> 7 rs35532309 159360755 RS35532309 chr1_1593… CRP 6.11e-5 CRP #> 8 rs6692378 159369451 RS6692378 chr1_1593… CRP 1.17e-6 CRP #> 9 rs10908714 159370563 RS10908714 chr1_1593… CRP 1.80e-5 CRP #> 10 rs6656924 159372915 RS6656924 chr1_1593… CRP 1.00e-6 CRP #> # ℹ 239 more rows #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes # search by variant - must be variantId (not rsid) get_significant_single_tissue_eqtls(variantIds = \"chr1_153209640_C_A_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 2 #> # A tibble: 2 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs1410858 153209640 RS1410858 chr1_15320… LOR 5.47e- 5 LOR #> 2 rs1410858 153209640 RS1410858 chr1_15320… PRR9 5.35e-19 PRR9 #> # ℹ 6 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes # filter by gene/variant and tissue site - either `gencodeIds` or `variantIds` # should be supplied as a minimum get_significant_single_tissue_eqtls(gencodeIds = c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"), variantIds = \"chr1_153209640_C_A_b38\", tissueSiteDetailIds = \"Whole_Blood\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 13 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper datasetId #> #> 1 rs14… 1.53e8 RS1410858 chr1_153… LOR 5.47e-5 LOR gtex_v8 #> # ℹ 5 more variables: tissueSiteDetailId , ontologyId , #> # chromosome , gencodeId , nes # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"Find significant single tissue eQTLs using Chromosomal Locations. service returns precomputed significant single tissue eQTLs. Results may filtered tissue, /dataset. default, service queries latest GTEx release. Since endpoint used support third party program portal, return structure different endpoints paginated. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"get_significant_single_tissue_eqtls_by_location( tissueSiteDetailId, start, end, chromosome, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_eqtls_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue eQTLs By Location — get_significant_single_tissue_eqtls_by_location","text":"","code":"# \\dontrun{ get_significant_single_tissue_eqtls_by_location( tissueSiteDetailId = \"Artery_Aorta\", start = 10000, end = 250000, chromosome = \"chr11\") #> # A tibble: 434 × 11 #> chromosome datasetId gencodeId geneSymbol geneSymbolUpper nes pValue #> #> 1 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.381 1.11e- 6 #> 2 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.364 2.25e- 6 #> 3 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.417 3.10e- 8 #> 4 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.480 8.39e- 9 #> 5 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> 6 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.553 8.89e-10 #> 7 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.577 2.95e-12 #> 8 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.547 6.13e-10 #> 9 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> 10 chr11 gtex_v8 ENSG000001779… BET1L BET1L 0.462 6.36e- 9 #> # ℹ 424 more rows #> # ℹ 4 more variables: pos , snpId , tissueSiteDetailId , #> # variantId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"Retrieve Interaction eQTL Data. service returns cell type interaction eQTLs (ieQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"get_significant_single_tissue_ieqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_ieqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Ieqtls — get_significant_single_tissue_ieqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_ieqtls(c(\"ENSG00000132693.12\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 86 #> # A tibble: 86 × 24 #> snpId bGISE pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #> #> 1 rs34188… 0.0890 1.54e8 RS34188388 0.102 0.00447 LOR LOR #> 2 rs24945… 0.0654 1.60e8 RS2494523 0.867 0.00129 CRP CRP #> 3 rs986760 0.148 1.53e8 RS986760 0.0454 0.00694 LOR LOR #> 4 rs17697… 0.0428 1.59e8 RS17697329 0.515 0.000627 CRP CRP #> 5 rs67415… 0.154 1.53e8 RS67415955 0.565 0.000754 LOR LOR #> 6 rs12133… 0.157 1.60e8 RS12133356 0.634 0.00106 CRP CRP #> 7 rs12132… 0.113 1.53e8 RS12132927 0.858 0.00365 LOR LOR #> 8 rs30269… 0.0683 1.59e8 RS3026943 0.684 0.00222 CRP CRP #> 9 rs24946… 0.0567 1.54e8 RS2494670 0.516 0.000595 LOR LOR #> 10 rs12121… 0.0695 1.60e8 RS12121609 0.444 0.000266 CRP CRP #> # ℹ 76 more rows #> # ℹ 16 more variables: pValueI , bGI , tissueSiteDetailId , #> # ontologyId , chromosome , tissueCellType , #> # tssDistance , bGSE , variantId , maf , bISE , #> # datasetId , bG , pValueAdjustedBH , bI , #> # gencodeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"Retrieve Interaction sQTL Data. service retrieves cell type interaction sQTLs (isQTLs), specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"get_significant_single_tissue_isqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_isqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"et Significant Single Tissue Isqtls — get_significant_single_tissue_isqtls","text":"","code":"# \\dontrun{ get_significant_single_tissue_isqtls(gencodeIds = c(\"ENSG00000065613.9\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 25 #> snpId bGISE pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper #> #> 1 rs4845790 0.0194 1.53e8 RS4845790 0.00645 8.97e-7 LOR LOR #> 2 rs4845790 0.0196 1.53e8 RS4845790 0.0118 1.41e-7 LOR LOR #> 3 rs359327… 0.0289 1.54e8 RS35932716 0.0142 3.70e-5 LOR LOR #> 4 rs146285… 0.0293 1.53e8 RS1462851… 0.0225 3.03e-5 LOR LOR #> # ℹ 17 more variables: pValueI , bGI , tissueSiteDetailId , #> # ontologyId , chromosome , tissueCellType , #> # tssDistance , bGSE , variantId , maf , bISE , #> # datasetId , bG , pValueAdjustedBH , bI , #> # gencodeId , phenotypeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"Retrieve Single Tissue sQTL Data. service returns single tissue sQTL data given genes, specified dataset. Results may filtered tissue default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"get_significant_single_tissue_sqtls( gencodeIds, variantIds = NULL, tissueSiteDetailIds = NULL, datasetId = \"gtex_v8\" )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). variantIds Character vector. Gtex variant IDs. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\".","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_significant_single_tissue_sqtls.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Significant Single Tissue Sqtls — get_significant_single_tissue_sqtls","text":"","code":"# \\dontrun{ # search by gene get_significant_single_tissue_sqtls(gencodeIds = c(\"ENSG00000065613.9\", \"ENSG00000203782.5\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 176 #> # A tibble: 176 × 14 #> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper #> #> 1 rs4636462 152442732 RS4636462 chr1_1524… LOR 7.71e-5 LOR #> 2 rs4845768 152442997 RS4845768 chr1_1524… LOR 6.57e-5 LOR #> 3 rs12069640 152444300 RS12069640 chr1_1524… LOR 7.13e-5 LOR #> 4 rs11803629 152445670 RS11803629 chr1_1524… LOR 1.81e-4 LOR #> 5 rs12125681 152445737 RS12125681 chr1_1524… LOR 1.81e-4 LOR #> 6 rs11205004 152446586 RS11205004 chr1_1524… LOR 1.81e-4 LOR #> 7 rs11579085 152447965 RS11579085 chr1_1524… LOR 1.81e-4 LOR #> 8 rs1885529 152448570 RS1885529 chr1_1524… LOR 1.81e-4 LOR #> 9 rs1885528 152448978 RS1885528 chr1_1524… LOR 1.81e-4 LOR #> 10 rs1885527 152449069 RS1885527 chr1_1524… LOR 1.81e-4 LOR #> # ℹ 166 more rows #> # ℹ 7 more variables: datasetId , tissueSiteDetailId , #> # ontologyId , chromosome , gencodeId , nes , #> # phenotypeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleux Gex — get_single_nucleus_gex","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"Retrieve Single Nucleus Gene Expression Data given Gene. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"get_single_nucleus_gex( gencodeIds, datasetId = \"gtex_snrnaseq_pilot\", tissueSiteDetailIds = NULL, excludeDataArray = TRUE, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. excludeDataArray String. Options TRUE FALSE page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleux Gex — get_single_nucleus_gex","text":"","code":"# \\dontrun{ # Search for one or more genes - returns a tibble with one row per tissue. # Column \"cellTypes\" now contains a tibble of expression summary data, with # one row for each cell type get_single_nucleus_gex(gencodeIds = c(\"ENSG00000203782.5\", \"ENSG00000132693.12\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 14 #> # A tibble: 14 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol cellTypes unit #> #> 1 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 2 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 3 Esophagus_Mucosa UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 4 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 5 Lung UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 6 Prostate UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 7 Skin_Sun_Exposed_L… UBERON:00… gtex_snr… ENSG0000… LOR log(… #> 8 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 9 Breast_Mammary_Tis… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 10 Esophagus_Mucosa UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 11 Esophagus_Muscular… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 12 Heart_Left_Ventric… UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 13 Lung UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 14 Prostate UBERON:00… gtex_snr… ENSG0000… CRP log(… # `excludeDataArray = FALSE` - expression values are stored under \"celltypes\" # in an additional column called \"data\" response <- get_single_nucleus_gex(gencodeIds = \"ENSG00000132693.12\", excludeDataArray = FALSE, itemsPerPage = 2) #> Warning: ! Total number of items (7) exceeds maximum page size (2). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 2 #> • totalNumberOfItems = 7 response #> # A tibble: 2 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol cellTypes unit #> #> 1 Muscle_Skeletal UBERON:00… gtex_snr… ENSG0000… CRP log(… #> 2 Breast_Mammary_Tiss… UBERON:00… gtex_snr… ENSG0000… CRP log(… # \"cellTypes\" contains a tibble of data with one row for each # cell type e.g. for Breast_Mammary_Tissue response$cellTypes[[2]] #> # A tibble: 2 × 8 #> cellType count meanWithZeros meanWithoutZeros medianWithZeros #> #> 1 Epithelial cell (luminal) 2 0.000902 2.19 0 #> 2 Endothelial cell (vascul… 1 0.00401 3.05 0 #> # ℹ 3 more variables: medianWithoutZeros , numZeros , data # when `excludeDataArray = FALSE`, expression values are stored in \"data\" # e.g. for Breast_Mammary_Tissue, Epithelial cell (luminal): response$cellTypes[[2]]$data[[1]] #> [1] 1.593315 2.782725 # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"Retrieve Summarized Single Nucleus Gene Expression Data. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"get_single_nucleus_gex_summary( datasetId = \"gtex_snrnaseq_pilot\", tissueSiteDetailIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_single_nucleus_gex_summary.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Single Nucleus Gex Summary — get_single_nucleus_gex_summary","text":"","code":"# \\dontrun{ # all tissues get_single_nucleus_gex_summary() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 114 #> # A tibble: 114 × 5 #> tissueSiteDetailId ontologyId datasetId cellType numCells #> #> 1 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. … 769 #> 2 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (NMJ-… 95 #> 3 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Endothelial c… 1124 #> 4 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Myocyte (sk. … 20772 #> 5 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Fibroblast 5944 #> 6 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Pericyte/SMC 448 #> 7 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Immune (DC/ma… 721 #> 8 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Adipocyte 159 #> 9 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Schwann cell 35 #> 10 Muscle_Skeletal UBERON:0011907 gtex_snrnaseq_pilot Satellite cell 487 #> # ℹ 104 more rows # filter for specific tissue get_single_nucleus_gex_summary(tissueSiteDetailIds = c(\"Breast_Mammary_Tissue\", \"Skin_Sun_Exposed_Lower_leg\")) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 25 #> # A tibble: 25 × 5 #> tissueSiteDetailId ontologyId datasetId cellType numCells #> #> 1 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Epithel… 4849 #> 2 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Adipocy… 1761 #> 3 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Immune … 358 #> 4 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Myoepit… 950 #> 5 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Fibrobl… 819 #> 6 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Endothe… 762 #> 7 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Endothe… 119 #> 8 Breast_Mammary_Tissue UBERON:0008367 gtex_snrnaseq_pi… Pericyt… 152 #> 9 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Sweat g… 300 #> 10 Skin_Sun_Exposed_Lower_leg UBERON:0004264 gtex_snrnaseq_pi… Epithel… 72 #> # ℹ 15 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sqtl Genes — get_sqtl_genes","title":"Get Sqtl Genes — get_sqtl_genes","text":"Retrieve sGenes (sQTL Genes). service returns sGenes (sQTL Genes) specified dataset. Results may filtered tissue. default, service queries latest GTEx release. retrieved data split pages items_per_page entries per page GTEx Portal API documentation.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"get_sqtl_genes( tissueSiteDetailId, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sqtl Genes — get_sqtl_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sqtl Genes — get_sqtl_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_sqtl_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Sqtl Genes — get_sqtl_genes","text":"","code":"# \\dontrun{ get_sqtl_genes(\"Whole_Blood\") #> Warning: ! Total number of items (3013) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 13 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 3013 #> # A tibble: 250 × 11 #> nPhenotypes pValueThreshold phenotypeId geneSymbol pValue datasetId #> #> 1 9 0.0000145 chr1:15947:16607:… WASH7P 7.15e- 8 gtex_v8 #> 2 6 0.00000634 chr1:1090428:1091… C1orf159 6.85e- 10 gtex_v8 #> 3 7 0.00000908 chr1:1228946:1231… SDF4 1.16e-188 gtex_v8 #> 4 6 0.00000861 chr1:1310688:1310… PUSL1 2.50e- 40 gtex_v8 #> 5 3 0.00000954 chr1:1325102:1327… CPTP 9.60e- 7 gtex_v8 #> 6 2 0.0000147 chr1:1487914:1489… ATAD3C 1.61e- 25 gtex_v8 #> 7 5 0.00000740 chr1:1487914:1489… ATAD3B 1.61e- 25 gtex_v8 #> 8 2 0.0000361 chr1:1545002:1547… SSU72 3.28e- 25 gtex_v8 #> 9 19 0.00000176 chr1:1629311:1629… MIB2 1.97e- 12 gtex_v8 #> 10 8 0.00000273 chr1:1641113:1641… CDK11B 3.08e- 56 gtex_v8 #> # ℹ 240 more rows #> # ℹ 5 more variables: empiricalPValue , tissueSiteDetailId , #> # ontologyId , qValue , gencodeId # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Subject — get_subject","title":"Get Subject — get_subject","text":"service returns information subjects used analyses datasets. Results may filtered dataset ID, subject ID, sex, age bracket Hardy Scale. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Subject — get_subject","text":"","code":"get_subject( datasetId = \"gtex_v8\", sex = NULL, ageBrackets = NULL, hardyScales = NULL, subjectIds = NULL, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Subject — get_subject","text":"datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". sex String. Options: \"male\", \"female\". ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". subjectIds Character vector. GTEx subject ID. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Subject — get_subject","text":"Tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Subject — get_subject","text":"","code":"# \\dontrun{ get_subject() #> Warning: ! Total number of items (979) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 4 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 979 #> # A tibble: 250 × 5 #> hardyScale ageBracket subjectId sex datasetId #> #> 1 Slow death 60-69 GTEX-1117F female gtex_v8 #> 2 Ventilator case 50-59 GTEX-111CU male gtex_v8 #> 3 Fast death - violent 60-69 GTEX-111FC male gtex_v8 #> 4 Intermediate death 60-69 GTEX-111VG male gtex_v8 #> 5 Ventilator case 60-69 GTEX-111YS male gtex_v8 #> 6 Ventilator case 60-69 GTEX-1122O female gtex_v8 #> 7 Fast death - natural causes 60-69 GTEX-1128S female gtex_v8 #> 8 NA 60-69 GTEX-113IC male gtex_v8 #> 9 Fast death - natural causes 50-59 GTEX-113JC female gtex_v8 #> 10 Fast death - natural causes 60-69 GTEX-117XS male gtex_v8 #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Tissue Site Detail — get_tissue_site_detail","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"Retrieve tissue site detail information database GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"get_tissue_site_detail(page = 0, itemsPerPage = 250)"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"tibble","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_tissue_site_detail.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Tissue Site Detail — get_tissue_site_detail","text":"","code":"# \\dontrun{ # returns a tibble with one row per tissue get_tissue_site_detail() #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 #> # A tibble: 54 × 18 #> tissueSiteDetailId colorHex colorRgb datasetId eGeneCount expressedGeneCount #> #> 1 Adipose_Subcutaneo… FF6600 255,102… gtex_v8 15607 28830 #> 2 Adipose_Visceral_O… FFAA00 255,170… gtex_v8 12482 28881 #> 3 Adrenal_Gland 33DD33 51,221,… gtex_v8 8123 28235 #> 4 Artery_Aorta FF5555 255,85,… gtex_v8 12493 28025 #> 5 Artery_Coronary FFAA99 255,170… gtex_v8 6296 28462 #> 6 Artery_Tibial FF0000 255,0,0 gtex_v8 15008 27217 #> 7 Bladder AA0000 170,0,0 gtex_v8 NA 28949 #> 8 Brain_Amygdala EEEE00 238,238… gtex_v8 3726 28196 #> 9 Brain_Anterior_cin… EEEE00 238,238… gtex_v8 5640 28921 #> 10 Brain_Caudate_basa… EEEE00 238,238… gtex_v8 8362 29230 #> # ℹ 44 more rows #> # ℹ 12 more variables: hasEGenes , hasSGenes , mappedInHubmap , #> # eqtlSampleSummary , rnaSeqSampleSummary , sGeneCount , #> # samplingSite , tissueSite , tissueSiteDetail , #> # tissueSiteDetailAbbr , ontologyId , ontologyIri # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns bladder_site_details <- get_tissue_site_detail() |> dplyr::filter(tissueSiteDetailId == \"Bladder\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 54 purrr::pluck(bladder_site_details, \"eqtlSampleSummary\", 1) #> $totalCount #> [1] 21 #> #> $female #> $female$ageMax #> [1] 59 #> #> $female$ageMin #> [1] 27 #> #> $female$ageMean #> [1] 43.6 #> #> $female$count #> [1] 7 #> #> #> $male #> $male$ageMax #> [1] 61 #> #> $male$ageMin #> [1] 21 #> #> $male$ageMean #> [1] 46 #> #> $male$count #> [1] 14 #> #> purrr::pluck(bladder_site_details, \"rnaSeqSampleSummary\", 1) #> $totalCount #> [1] 21 #> #> $female #> $female$ageMax #> [1] 59 #> #> $female$ageMin #> [1] 27 #> #> $female$ageMean #> [1] 43.6 #> #> $female$count #> [1] 7 #> #> #> $male #> $male$ageMax #> [1] 61 #> #> $male$ageMin #> [1] 21 #> #> $male$ageMean #> [1] 46 #> #> $male$count #> [1] 14 #> #> # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Top Expressed Genes — get_top_expressed_genes","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"Find top expressed genes specified tissue. Returns top expressed genes specified tissue dataset, sorted median expression. optional parameter filterMtGene set true, mitochondrial genes excluded results. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"get_top_expressed_genes( tissueSiteDetailId, datasetId = \"gtex_v8\", filterMtGene = TRUE, page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". filterMtGene Logical. Exclude mitochondrial genes. page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_top_expressed_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Top Expressed Genes — get_top_expressed_genes","text":"","code":"# \\dontrun{ get_top_expressed_genes(tissueSiteDetailId = \"Artery_Aorta\") #> Warning: ! Total number of items (56163) exceeds maximum page size (250). #> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 225 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 56163 #> # A tibble: 250 × 7 #> tissueSiteDetailId ontologyId datasetId gencodeId geneSymbol median unit #> #> 1 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… MGP 11936. TPM #> 2 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… FTL 9196. TPM #> 3 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… ACTB 9154. TPM #> 4 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… BGN 8167. TPM #> 5 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… TAGLN 6099. TPM #> 6 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… ACTA2 5736. TPM #> 7 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… IGFBP7 5639. TPM #> 8 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… MYL9 4275. TPM #> 9 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… HSPB1 3780. TPM #> 10 Artery_Aorta UBERON:0001496 gtex_v8 ENSG0000… FLNA 3732. TPM #> # ℹ 240 more rows # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Transcripts — get_transcripts","title":"Get Transcripts — get_transcripts","text":"Find transcripts reference gene. service returns information transcripts given versioned GENCODE ID. genome build GENCODE version must provided. default, service queries genome build GENCODE version used latest GTEx release. GTEx API Portal documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Transcripts — get_transcripts","text":"","code":"get_transcripts( gencodeId, gencodeVersion = \"v26\", genomeBuild = \"GRCh38/hg38\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Transcripts — get_transcripts","text":"gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Transcripts — get_transcripts","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_transcripts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Transcripts — get_transcripts","text":"","code":"# \\dontrun{ get_transcripts(gencodeId = \"ENSG00000203782.5\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 11 #> start end featureType genomeBuild transcriptId source chromosome gencodeId #> #> 1 1.53e8 1.53e8 transcript GRCh38/hg38 ENST0000036… HAVANA chr1 ENSG0000… #> # ℹ 3 more variables: geneSymbol , gencodeVersion , strand # }"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant — get_variant","title":"Get Variant — get_variant","text":"service returns information variant, including position, dbSNP RS ID, reference allele, alternative allele, whether minor allele frequency >= 1%. GTEx v6p, also information whether whole exome sequence chip sequencing data available. Results may queried GTEx variant ID (variantId), dbSNP RS ID (snpId) genomic location (chromosome pos). Variants identified based genotype data dataset cohort, namely, dataset-dependent. variant assigned unique GTEx variant ID (.e. primary key). variants mappable dbSNP RS ID. default, service queries latest GTEx release. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant — get_variant","text":"","code":"get_variant( snpId = NULL, variantId = NULL, chromosome = NULL, pos = NULL, datasetId = \"gtex_v8\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant — get_variant","text":"snpId String variantId String. gtex variant ID. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". pos Integer, vector. datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant — get_variant","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant — get_variant","text":"","code":"# search by rsid get_variant(snpId = \"rs1410858\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> # ℹ 2 more variables: datasetId , ref # search by variantId get_variant(variantId = \"chr1_153209640_C_A_b38\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 1 #> # A tibble: 1 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs1410858 1_153182116_C_A_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> # ℹ 2 more variables: datasetId , ref # search by chromosome and position get_variant(chromosome = \"chr1\", pos = 153209600:153209700) #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs11205220 1_153182115_T_… 1.53e8 TRUE chr1_153… C chr1 RS11205220 #> 2 rs1410858 1_153182116_C_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T chr1 RS1392967… #> 4 rs80104092 1_153182149_T_… 1.53e8 FALSE chr1_153… C chr1 RS80104092 #> # ℹ 2 more variables: datasetId , ref "},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variant By Location — get_variant_by_location","title":"Get Variant By Location — get_variant_by_location","text":"service allows user query information variants certain chromosome certain location. GTEx Portal API documentation","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location( start, end, chromosome, sortBy = \"pos\", sortDirection = \"asc\", page = 0, itemsPerPage = 250 )"},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variant By Location — get_variant_by_location","text":"start Integer. end Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". page Integer (default = 0). itemsPerPage Integer (default = 250).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variant By Location — get_variant_by_location","text":"tibble.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/get_variant_by_location.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variant By Location — get_variant_by_location","text":"","code":"get_variant_by_location(start = 153209600, end = 153209700, chromosome = \"chr1\") #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 1 #> • page = 0 #> • maxItemsPerPage = 250 #> • totalNumberOfItems = 4 #> # A tibble: 4 × 10 #> snpId b37VariantId pos maf01 variantId alt chromosome snpIdUpper #> #> 1 rs11205220 1_153182115_T_… 1.53e8 TRUE chr1_153… C chr1 RS11205220 #> 2 rs1410858 1_153182116_C_… 1.53e8 TRUE chr1_153… A chr1 RS1410858 #> 3 rs139296761 1_153182120_C_… 1.53e8 FALSE chr1_153… T chr1 RS1392967… #> 4 rs80104092 1_153182149_T_… 1.53e8 FALSE chr1_153… C chr1 RS80104092 #> # ℹ 2 more variables: datasetId , ref "},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr: Query the GTEx Portal API — gtexr-package","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"convenient R interface Genotype-Tissue Expression (GTEx) Portal API. information API, see https://gtexportal.org/api/v2/redoc.","code":""},{"path":[]},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gtexr: Query the GTEx Portal API — gtexr-package","text":"Maintainer: Alasdair Warwick alasdair.warwick.19@ucl.ac.uk (ORCID) [copyright holder] Authors: Benjamin Zuckerman (ORCID) Abraham Olvera-Barrios (ORCID) Chuin Ying Ung (ORCID) Robert Luben (ORCID)","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"gtexr arguments — gtexr_arguments","title":"gtexr arguments — gtexr_arguments","text":"Internal function documents arguments exported gtexr functions wrap GTEx Portal API endpoints (using roxygen @inheritParams tag).","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gtexr arguments — gtexr_arguments","text":"","code":"gtexr_arguments( ageBrackets = NULL, aliquotIds = NULL, attributeSubset = NULL, autolysisScores = NULL, cellType = NULL, bp_window = NULL, chromosome = NULL, datasetId = NULL, dataTypes = NULL, draw = NULL, end = NULL, excludeDataArray = NULL, .featureId = NULL, filterMtGene = NULL, gencodeId = NULL, gencodeIds = NULL, gencodeVersion = NULL, geneId = NULL, geneIds = NULL, genomeBuild = NULL, hardyScales = NULL, hasExpressionData = NULL, hasGenotype = NULL, itemsPerPage = NULL, ischemicTime = NULL, ischemicTimeGroups = NULL, materialTypes = NULL, organizationName = NULL, page = NULL, pathCategory = NULL, phenotypeId = NULL, pos = NULL, project_id = NULL, rin = NULL, sampleId = NULL, sampleIds = NULL, searchTerm = NULL, sex = NULL, snpId = NULL, sortBy = NULL, sortDirection = NULL, start = NULL, subjectIds = NULL, tissueSampleIds = NULL, tissueSiteDetailId = NULL, tissueSiteDetailIds = NULL, uberonIds = NULL, variantId = NULL, variantIds = NULL )"},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gtexr arguments — gtexr_arguments","text":"ageBrackets age bracket(s) donors interest. Options: \"20-29\", \"30-39\", \"40-49\", \"50-59\", \"60-69\", \"70-79\". aliquotIds Character vector. attributeSubset String. Examples include limited \"sex\", \"ageBracket\" autolysisScores Character vector. Options: \"None\", \"Mild\", \"Moderate\", \"Severe\". cellType String. \"Adipocytes\", \"Epithelial_cells\", \"Hepatocytes\", \"Keratinocytes\", \"Myocytes\", \"Neurons\", \"Neutrophils\". bp_window Integer. chromosome String. One \"chr1\", \"chr2\", \"chr3\", \"chr4\", \"chr5\", \"chr6\", \"chr7\", \"chr8\", \"chr9\", \"chr10\", \"chr11\", \"chr12\", \"chr13\", \"chr14\", \"chr15\", \"chr16\", \"chr17\", \"chr18\", \"chr19\", \"chr20\", \"chr21\", \"chr22\", \"chrM\", \"chrX\", \"chrY\". datasetId String. Unique identifier dataset. Usually includes data source data release. Options: \"gtex_v8\", \"gtex_snrnaseq_pilot\". dataTypes Character vector. Options: \"RNASEQ\", \"WGS\", \"WES\", \"OMNI\", \"EXCLUDE\". draw Integer. end Integer. excludeDataArray String. Options TRUE FALSE .featureId String. genomic feature e.g. GENCODE ID, RSID GTEx Variant ID. filterMtGene Logical. Exclude mitochondrial genes. gencodeId String. Versioned GENCODE ID gene, e.g. \"ENSG00000065613.9\". gencodeIds character vector Versioned GENCODE IDs, e.g. c(\"ENSG00000132693.12\", \"ENSG00000203782.5\"). gencodeVersion String (default = \"v26\"). GENCODE annotation release. Either \"v26\" \"v19\". geneId String. gene symbol, gencode ID, Ensemble ID. geneIds character vector gene symbols, versioned gencodeIds, unversioned gencodeIds. genomeBuild String. Options: \"GRCh38/hg38\", \"GRCh37/hg19\". Default = \"GRCh38/hg38\". hardyScales Character vector. list Hardy Scale(s) interest. Options: \"Ventilator case\", \"Fast death - violent\", \"Fast death - natural causes\", \"Intermediate death\", \"Slow death\". hasExpressionData Logical. hasGenotype Logical. itemsPerPage Integer (default = 250). ischemicTime Integer. ischemicTimeGroups Character vector. Options: \"<= 0\", \"1 - 300\", \"301 - 600\", \"601 - 900\", \"901 - 1200\", \"1201 - 1500\", \"> 1500\". materialTypes String, vector. Options: \"Cells:Cell Line Viable\", \"DNA:DNA Genomic\", \"DNA:DNA Somatic\", \"RNA:Total RNA\", \"Tissue:PAXgene Preserved\", \"Tissue:PAXgene Preserved Paraffin-embedded\", \"Tissue:Fresh Frozen Tissue\". organizationName String. Options: \"GTEx Consortium\" \"Kid's First\". page Integer (default = 0). pathCategory Character vector. Options: \"adenoma\", \"amylacea\", \"atelectasis\", \"atherosclerosis\", \"atherosis\", \"atrophy\", \"calcification\", \"cirrhosis\", \"clean_specimens\", \"congestion\", \"corpora_albicantia\", \"cyst\", \"desquamation\", \"diabetic\", \"dysplasia\", \"edema\", \"emphysema\", \"esophagitis\", \"fibrosis\", \"gastritis\", \"glomerulosclerosis\", \"goiter\", \"gynecomastoid\", \"hashimoto\", \"heart_failure_cells\", \"hemorrhage\", \"hepatitis\", \"hyalinization\", \"hypereosinophilia\", \"hyperplasia\", \"hypertrophy\", \"hypoxic\", \"infarction\", \"inflammation\", \"ischemic_changes\", \"macrophages\", \"mastopathy\", \"metaplasia\", \"monckeberg\", \"necrosis\", \"nephritis\", \"nephrosclerosis\", \"no_abnormalities\", \"nodularity\", \"pancreatitis\", \"pigment\", \"pneumonia\", \"post_menopausal\", \"prostatitis\", \"saponification\", \"scarring\", \"sclerotic\", \"solar_elastosis\", \"spermatogenesis\", \"steatosis\", \"sweat_glands\", \"tma\". phenotypeId String. See GTEx portal FAQs details. pos Integer, vector. project_id String. Options: \"gtex\", \"adult-gtex\", \"egtex\". rin Integer vector. sampleId String. ^GTEX-[-Z0-9]{5}-[0-9]{4}-SM-[-Z0-9]{5}$ sampleIds Character vector. GTEx sample ID. searchTerm String. sex String. Options: \"male\", \"female\". snpId String sortBy String. Options: \"sampleId\", \"ischemicTime\", \"aliquotId\", \"tissueSampleId\", \"hardyScale\", \"pathologyNotes\", \"ageBracket\", \"tissueSiteDetailId\", \"sex\". sortDirection String. Options: \"asc\", \"desc\". Default = \"asc\". start Integer. subjectIds Character vector. GTEx subject ID. tissueSampleIds Array strings. list Tissue Sample ID(s). tissueSiteDetailId String. ID tissue interest. Can GTEx specific ID (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology ID. tissueSiteDetailIds Character vector IDs tissues interest. Can GTEx specific IDs (e.g. \"Whole_Blood\"; use get_tissue_site_detail() see valid values) Ontology IDs. uberonIds Character vector Uberon IDs (e.g. \"UBERON:EFO_0000572\"; use get_tissue_site_detail() see valid values). variantId String. gtex variant ID. variantIds Character vector. Gtex variant IDs.","code":""},{"path":"https://rmgpanw.github.io/gtexr/reference/gtexr_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gtexr arguments — gtexr_arguments","text":"Returns NULL invisibly. Used documentation .","code":""},{"path":"https://rmgpanw.github.io/gtexr/news/index.html","id":"gtexr-development-version","dir":"Changelog","previous_headings":"","what":"gtexr (development version)","title":"gtexr (development version)","text":"Added NEWS.md file track changes package.","code":""}]