various typo and documentation fixes; also update getdownloads_page_d…

…ata(), get_file_list(), get_significantTissueEqtlByLocation() and get_linkage_disequilibrium_data()
rmgpanw · Apr 16, 2024 · 836b938 · 836b938
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diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+.Rproj.user
+docs
+.Rhistory
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,29 @@
+Package: gtexr
+Title: Query the GTEx Portal API
+Version: 0.0.0.9000
+Authors@R: 
+    person(given = "Alasdair",
+           family = "Warwick",
+           role = c("aut", "cre", "cph"),
+           email = "alasdair.warwick06@gmail.com",
+           comment = c(ORCID = "0000-0002-0800-2890"))
+Description: A convenient R interface to the GTEx Portal API.
+License: MIT + file LICENSE
+URL: https://rmgpanw.github.io/gtexr/,
+    https://github.com/rmgpanw/gtexr
+BugReports: https://github.com/rmgpanw/gtexr/issues
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Imports: 
+    cli,
+    dplyr,
+    httr2 (>= 1.0.0),
+    purrr,
+    rlang,
+    tibble,
+    tidyr
+Suggests: 
+    httptest2,
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: gtexr authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 gtexr authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,38 @@
+# Generated by roxygen2: do not edit by hand
+
+export(available_tissueSiteDetailIds)
+export(calculate_eqtls)
+export(get_annotation)
+export(get_collapsed_gene_model_exon)
+export(get_dataset_info)
+export(get_downloads_page_data)
+export(get_eqtl_genes)
+export(get_exons)
+export(get_file_list)
+export(get_fine_mapping)
+export(get_full_get_collapsed_gene_model_exon)
+export(get_functional_annotation)
+export(get_gene_search)
+export(get_genes)
+export(get_gwas_catalog_by_location)
+export(get_image)
+export(get_independent_eqtl)
+export(get_linkage_disequilibrium_by_variant_data)
+export(get_linkage_disequilibrium_data)
+export(get_maintenance_message)
+export(get_multi_tissue_eqtls)
+export(get_neighbor_gene)
+export(get_news_item)
+export(get_sample)
+export(get_service_info)
+export(get_significant_single_tissue_eqtls)
+export(get_significant_single_tissue_eqtls_by_location)
+export(get_significant_single_tissue_ieqtls)
+export(get_significant_single_tissue_isqtls)
+export(get_significant_single_tissue_sqtls)
+export(get_sqtl_genes)
+export(get_subject)
+export(get_tissue_site_detail)
+export(get_transcripts)
+export(get_variant)
+export(get_variant_by_location)
diff --git a/R/calculate_eqtls.R b/R/calculate_eqtls.R
@@ -3,6 +3,11 @@
 #' [Calculate your own
 #' eQTLs](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_expression_quantitative_trait_loci_api_v2_association_dyneqtl_get)
 #'
+#' Notes on output:
+#'
+#' * Beta and standard error are recorded in columns `nes` and `error` respectively (see [GTEx FAQs](https://gtexportal.org/home/faq#nes_beta))
+#' * `variantId` contains (in order) chromosome, position, reference allele, alternative allele and human genome build separated by underscores. The reference and alternative alleles for "chr1_13550_G_A_b38" for example are "G" and "A" respectively.
+#'
 #' @inheritParams gtexr_arguments
 #'
 #' @return A tibble.

diff --git a/R/get_annotation.R b/R/get_annotation.R
@@ -1,21 +1,19 @@
 #'Get Annotation
 #'
 #'@description
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_annotation_api_v2_dataset_annotation_get
 #' - This service returns the list of annotations and allowed values by which a particular dataset can be subsetted.
 #' - Results may be filtered by dataset.
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_annotation_api_v2_dataset_annotation_get
+#'[GTEx Portal API
+#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_annotation_api_v2_dataset_annotation_get)
+#'
 #'@inheritParams gtexr_arguments
 #'
 #'@return A tibble
 #'@export
 #'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_annotation()
 get_annotation <- function(datasetId = "gtex_v8",
                            page = 0,

diff --git a/R/get_collapsed_gene_model_exon.R b/R/get_collapsed_gene_model_exon.R
@@ -8,8 +8,7 @@
 #'algorithm developed by the GTEx analysis team.
 #' - By default, this service queries the models used by the latest GTEx release.
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_collapsed_gene_model_exon_api_v2_dataset_collapsedGeneModelExon_get
+#'[GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_collapsed_gene_model_exon_api_v2_dataset_collapsedGeneModelExon_get)
 #'
 #'@inheritParams gtexr_arguments
 #'
@@ -18,7 +17,6 @@
 #'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_collapsed_gene_model_exon(gencodeIds = c("ENSG00000132693.12",
 #'                                                   "ENSG00000203782.5"))
 get_collapsed_gene_model_exon <- function(gencodeIds,

diff --git a/R/get_downloads_page_data.R b/R/get_downloads_page_data.R
@@ -3,18 +3,20 @@
 #'@description
 #' - Retrieves all the files belonging to the given project_id for display on the Downloads Page
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_downloads_page_data_api_v2_dataset_openAccessFilesMetadata_get
+#'[GTEx Portal API
+#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_downloads_page_data_api_v2_dataset_openAccessFilesMetadata_get)
 #'
 #'@inheritParams gtexr_arguments
 #'
 #'@return A Tibble
 #'@export
-#'@family Dataset Endpoints
+#'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_downloads_page_data()
-get_downloads_page_data <- function(project_id = "gtex"){
-  gtex_query(endpoint = "dataset/openAccessFilesMetaData")
+get_downloads_page_data <- function(project_id = "adult-gtex") {
+  gtex_query(endpoint = "dataset/openAccessFilesMetadata",
+             return_raw = TRUE)$data |>
+    purrr::map(tibble::as_tibble) |>
+    dplyr::bind_rows()
 }
diff --git a/R/get_file_list.R b/R/get_file_list.R
@@ -1,19 +1,21 @@
 #' Get File List
+#'
 #' @description
 #' - Get all the files in GTEx dataset for Download page
 #'
-#' [GTEx Portal API documentation]
-#' https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_file_list_api_v2_dataset_fileList_get
+#' [GTEx Portal API
+#' documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_file_list_api_v2_dataset_fileList_get)
 #'
-#'@inheritParams gtexr_arguments
 #'
 #' @return A Tibble
 #' @export
 #' @family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_file_list()
-get_file_list <- function(){
-  gtex_query(enpoint = "dataset/fileList")
+get_file_list <- function() {
+  gtex_query(endpoint = "dataset/fileList",
+             return_raw = TRUE) |>
+    purrr::map(tibble::as_tibble) |>
+    dplyr::bind_rows()
 }
diff --git a/R/get_fine_mapping.R b/R/get_fine_mapping.R
@@ -17,7 +17,6 @@
 #'@family Static Association Endpoints
 #'
 #' @examples
-#' \dontrun{
 #' # search by gene
 #' get_fine_mapping(gencodeIds = c("ENSG00000132693.12",
 #'                                "ENSG00000203782.5"))
@@ -28,7 +27,6 @@
 #'                  variantId = "chr1_153228363_A_G_b38",
 #'                  tissueSiteDetailIds = c("Whole_Blood",
 #'                                         "Thyroid"))
-#'}
 get_fine_mapping <- function(gencodeIds,
                              datasetId = "gtex_v8",
                              variantId = NULL,

diff --git a/R/get_full_get_collapsed_gene_model_exon.R b/R/get_full_get_collapsed_gene_model_exon.R
@@ -3,17 +3,16 @@
 #'@description
 #' - This service allows the user to query the full Collapsed Gene Model Exon of a specific gene by gencode ID
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_full_get_collapsed_gene_model_exon_api_v2_dataset_fullCollapsedGeneModelExon_get
+#'[GTEx Portal API
+#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_full_get_collapsed_gene_model_exon_api_v2_dataset_fullCollapsedGeneModelExon_get)
 #'
 #'@inheritParams gtexr_arguments
 #'
 #'@return A Tibble
 #'@export
-#'@family Dataset Endpoints
+#'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_full_get_collapsed_gene_model_exon(gencodeIds = c("ENSG00000132693.12",
 #'                                                   "ENSG00000203782.5"))
 get_full_get_collapsed_gene_model_exon <- function(gencodeIds,

diff --git a/R/get_functional_annotation.R b/R/get_functional_annotation.R
@@ -3,16 +3,15 @@
 #'@description
 #' - This endpoint retrieves the functional annotation of a certain chromosome location. Default to most recent dataset release.
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_full_get_collapsed_gene_model_exon_api_v2_dataset_fullCollapsedGeneModelExon_get
+#'[GTEx Portal API
+#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_full_get_collapsed_gene_model_exon_api_v2_dataset_fullCollapsedGeneModelExon_get)
 #'
 #'@inheritParams gtexr_arguments
 #'@return A Tibble
 #'@export
-#'@family Dataset Endpoints
+#'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_functional_annotation(chromosome = "chr15", start = 1400, end = 20000)
 get_functional_annotation <- function(datasetId = "gtex_v8",
                                       chromosome,

diff --git a/R/get_image.R b/R/get_image.R
@@ -8,8 +8,8 @@
 #'
 #' @examples
 #' get_image()
-#' get_image(tissueSampleId = "GTEX-1117F-0226", page = 0, itemsPerPage = 100000)
-get_image <- function(tissueSampleId = NULL,
+#' get_image(tissueSampleIds = "GTEX-1117F-0226", page = 0, itemsPerPage = 100000)
+get_image <- function(tissueSampleIds = NULL,
                       page = 0,
                       itemsPerPage = 250) {
   gtex_query(endpoint = "histology/image")

diff --git a/R/get_independent_eqtl.R b/R/get_independent_eqtl.R
@@ -2,12 +2,12 @@
 #'
 #'@description Retrieve Independent eQTL Data
 #'
-#'  Finds and returns Independent eQTL Data data for the provided list of genes
-#'  By default, this endpoint fetches data from the latest GTEx version The
-#'  retrieved data is split into pages with items_per_page entries per page
+#' - Finds and returns Independent eQTL Data data for the provided list of genes
+#' - By default, this endpoint fetches data from the latest GTEx version
 #'
-#'  [GTEx portal API documentation]
-#'  (https://gtexportal.org/api/v2/redoc#tag/Static-Association-Endpoints/operation/get_independent_eqtl_api_v2_association_independentEqtl_get)
+#'  The retrieved data is split into pages with items_per_page entries per page
+#'
+#' [GTEx portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Static-Association-Endpoints/operation/get_independent_eqtl_api_v2_association_independentEqtl_get)
 #'
 #'@inheritParams gtexr_arguments
 #'
@@ -16,19 +16,17 @@
 #'@family Static Association Endpoints
 #'
 #' @examples
-#' \dontrun{
 #' # search by gene
 #' get_independent_eqtl(gencodeIds = c("ENSG00000132693.12",
 #'                                "ENSG00000203782.5"))
 #'
 #' # 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"))
-#'}
-get_independent_eqtl <- function(gencodeId,
-                                 tissueSiteDetailId = NULL,
+#'                                     "ENSG00000203782.5"),
+#'                      tissueSiteDetailIds = c("Whole_Blood",
+#'                                              "Thyroid"))
+get_independent_eqtl <- function(gencodeIds,
+                                 tissueSiteDetailIds = NULL,
                                  datasetId = "gtex_v8",
                                  page = 0,
                                  itemsPerPage = 250){

diff --git a/R/get_linkage_disequilibrium_by_variant_data.R b/R/get_linkage_disequilibrium_by_variant_data.R
@@ -1,20 +1,19 @@
-#' Get Linkage Disequilibrium By Variant Data
+#'Get Linkage Disequilibrium By Variant Data
 #'
-#' @description
+#'@description
 #' - Find linkage disequilibrium (LD) data for a given variant
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_linkage_disequilibrium_by_variant_data_api_v2_dataset_ldByVariant_get
+#'[GTEx Portal API
+#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_linkage_disequilibrium_by_variant_data_api_v2_dataset_ldByVariant_get)
 #'
 #'@inheritParams gtexr_arguments
 #'@return A Tibble
 #'@export
-#'@family Dataset Endpoints
+#'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_linkage_disequilibrium_by_variant_data()
-get_linkage_disequilibirum_by_variant_data <- function(variantId = NULL,
+get_linkage_disequilibrium_by_variant_data <- function(variantId = NULL,
                                                       page = 0,
                                                       itemsPerPage = 250){
   gtex_query(endpoint = "dataset/ldByVariant")

diff --git a/R/get_linkage_disequiliribum_data.R → R/get_linkage_disequilibrium_data.R b/R/get_linkage_disequiliribum_data.R → R/get_linkage_disequilibrium_data.R
@@ -1,26 +1,32 @@
-#'Get Linkage Disequilibrium Data
+#' Get Linkage Disequilibrium Data
 #'
-#'@description
+#' @description
 #' - Find linkage disequilibrium (LD) data for a given gene.
 #' - This endpoint returns linkage disequilibrium data for the cis-eQTLs found associated with the provided gene in a specified dataset.
 #' - Results are queried by gencode ID. By default, the service queries the latest GTEx release.
 #' - Specify a dataset ID to fetch results from a different dataset.
 #'
-#'[GTEx Portal API documentation]
-#'https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_variant_by_location_api_v2_dataset_variantByLocation_get#'
+#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_variant_by_location_api_v2_dataset_variantByLocation_get)
 #'
-#'@inheritParams gtexr_arguments
-#'@return A Tibble
-#'@export
-#'@family Dataset Endpoints
+#' @inheritParams gtexr_arguments
+#' @return A tibble.
+#' @export
+#'@family Datasets Endpoints
 #'
 #' @examples
-#' \dontrun
 #' get_linkage_disequilibrium_data(gencodeIds = c("ENSG00000132693.12",
 #'                                                   "ENSG00000203782.5"))
-get_linkage_disequilibirum_data <- function(gencodeIds,
+get_linkage_disequilibrium_data <- function(gencodeIds,
                                             datasetId = "gtex_v8",
                                             page = 0,
                                             itemsPerPage = 250){
-  gtex_query(endpoint = "dataset/ld")
+  gtex_query(endpoint = "dataset/ld",
+             return_raw = TRUE)$data |>
+    purrr::map(\(x) tibble::tibble(variants = x[[1]], ld = x[[2]])) |>
+    dplyr::bind_rows() |>
+    tidyr::separate_wider_delim(
+      cols = "variants",
+      delim = ",",
+      names = c("variantId_1", "variantId_2")
+    )
 }