various tidying/fixes pre-CRAN submission (#13)

rmgpanw · Sep 18, 2024 · 3aef357 · 3aef357
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^.vscode$
 ^doc$
 ^Meta$
+^cran-comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,24 @@
 Package: gtexr
 Title: Query the GTEx Portal API
 Version: 0.0.0.9000
-Authors@R: 
+Authors@R: c(
     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.
+           email = "alasdair.warwick.19@ucl.ac.uk",
+           comment = c(ORCID = "0000-0002-0800-2890")),
+    person("Benjamin", "Zuckerman", role = "aut",
+           comment = c(ORCID = "0000-0002-0077-6074")),
+    person("Abraham", "Olvera-Barrios", role = "aut",
+           comment = c(ORCID = "0000-0002-3305-4465")),
+    person("Chuin Ying", "Ung", role = "aut",
+           comment = c(ORCID = "0000-0001-8487-4589")),
+    person("Robert", "Luben", role = "aut",
+           comment = c(ORCID = "0000-0002-5088-6343"))
+    )
+Description: A convenient R interface to the Genotype-Tissue Expression (GTEx) 
+    Portal API. For more information on the API, see 
+    <https://gtexportal.org/api/v2/redoc>.
 License: MIT + file LICENSE
 URL: https://rmgpanw.github.io/gtexr/,
     https://github.com/rmgpanw/gtexr

diff --git a/R/get_sample.R → R/get_sample_datasets_endpoints.R b/R/get_sample.R → R/get_sample_datasets_endpoints.R
diff --git a/R/gtexr_arguments.R b/R/gtexr_arguments.R
@@ -81,35 +81,69 @@
 #' @param sortDirection String. Options: "asc", "desc". Default = "asc".
 #' @param start Integer.
 #' @param subjectIds Character vector. GTEx subject ID.
-#' @param tissueSampleId String. A Tissue Sample ID.
 #' @param tissueSampleIds Array of strings. A list of Tissue Sample ID(s).
 #' @param tissueSiteDetailId String. The ID of the tissue of interest. Can be a
 #'   GTEx specific ID (e.g. "Whole_Blood"; use [get_tissue_site_detail()]
 #'   to see valid values) or an Ontology ID.
 #' @param tissueSiteDetailIds Character vector of IDs for tissues of interest.
 #'   Can be GTEx specific IDs (e.g. "Whole_Blood"; use
 #'   [get_tissue_site_detail()] to see valid values) or Ontology IDs.
-#' @param uberonIds Character vector. A list of Uberon ID(s) of interest.
-#'   Options: "UBERON:EFO_0000572", "UBERON:EFO_0002009", "UBERON:0000007",
-#'   "UBERON:0000458", "UBERON:0000473", "UBERON:0000945", "UBERON:0000992",
-#'   "UBERON:0000995", "UBERON:0000996", "UBERON:0001114", "UBERON:0001150",
-#'   "UBERON:0001157", "UBERON:0001159", "UBERON:0001211", "UBERON:0001225",
-#'   "UBERON:0001255", "UBERON:0001293", "UBERON:0001323", "UBERON:0001496",
-#'   "UBERON:0001621", "UBERON:0001870", "UBERON:0001873", "UBERON:0001874",
-#'   "UBERON:0001876", "UBERON:0001882", "UBERON:0001898", "UBERON:0001954",
-#'   "UBERON:0002037", "UBERON:0002038", "UBERON:0002046", "UBERON:0002106",
-#'   "UBERON:0002190", "UBERON:0002367", "UBERON:0002369", "UBERON:0003889",
-#'   "UBERON:0004264", "UBERON:0004550", "UBERON:0004648", "UBERON:0006330",
-#'   "UBERON:0006469", "UBERON:0006566", "UBERON:0006631", "UBERON:0006920",
-#'   "UBERON:0007610", "UBERON:0008367", "UBERON:0008952", "UBERON:0009834",
-#'   "UBERON:0009835", "UBERON:0010414", "UBERON:0011907", "UBERON:0012249",
-#'   "UBERON:0013756", "UBERON:0036149".
+#' @param uberonIds Character vector of Uberon IDs (e.g. "UBERON:EFO_0000572";
+#'   use [get_tissue_site_detail()] to see valid values).
 #' @param variantId String. A gtex variant ID.
 #' @param variantIds Character vector. Gtex variant IDs.
 #'
 #' @keywords internal
 #' @return Returns `NULL` invisibly. Used for documentation only.
-gtexr_arguments <- function() {
+gtexr_arguments <- function(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) {
   tibble::tribble(
     ~arg, ~type, ~scalar, ~pluralised, ~shinyinput, ~choices,
     "ageBrackets", "character", FALSE, TRUE, "selectInput", c("20-29", "30-39", "40-49", "50-59", "60-69", "70-79"),

diff --git a/README.Rmd b/README.Rmd
@@ -27,7 +27,13 @@ New to R? Try out the ⭐[shiny app](https://7hocgq-rmgpanw.shinyapps.io/gtexr/)
 
 ## Installation
 
-You can install the development version of gtexr from [GitHub](https://github.com/) with:
+You can install this package from CRAN:
+
+``` r
+install.packages("gtexr")
+```
+
+Or you can install the development version  of gtexr from [GitHub](https://github.com/rmgpanw/gtexr) with:
 
 ``` r
 # install.packages("devtools")

diff --git a/README.md b/README.md
@@ -23,8 +23,14 @@ app](https://7hocgq-rmgpanw.shinyapps.io/gtexr/)⭐.
 
 ## Installation
 
-You can install the development version of gtexr from
-[GitHub](https://github.com/) with:
+You can install this package from CRAN:
+
+``` r
+install.packages("gtexr")
+```
+
+Or you can install the development version of gtexr from
+[GitHub](https://github.com/rmgpanw/gtexr) with:
 
 ``` r
 # install.packages("devtools")

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
diff --git a/man/get_sample_datasets_endpoints.Rd b/man/get_sample_datasets_endpoints.Rd
diff --git a/man/gtexr-package.Rd b/man/gtexr-package.Rd
diff --git a/man/gtexr_arguments.Rd b/man/gtexr_arguments.Rd
diff --git a/vignettes/developer_guide.Rmd b/vignettes/developer_guide.Rmd
@@ -14,34 +14,21 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r setup}
-library(gtexr)
-```
-
-**WIP**
-
 ## Functions
 
-- [ ] Function name is title of endpoint in lower case, with words separated by underscores
-- [ ] `@description` section is copied verbatim from API documentation site and ends with a link to the corresponding API endpoint documentation.
-- [ ] Further notes may be added under `@details`
-- [ ] Arguments 
-
-  - [ ] Names match those for API endpoint, except where the argument accepts an array (vector in R) of values, in which case it is pluralised
-  - [ ] Note that the [Get Genomic Features] endpoint takes a path parameter "featureId". The corresponding gtexr argument is prefixed with "." (`.featureId`).
-  - [ ] Default values also match those for API endpoint
-  - [ ] Query parameters flagged as "required" in the GTEx Portal API documentation do not have default values. Note however that while `variantId` is not flagged as "required" for [Get Linkage Disequilibrium By Variant Data](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_linkage_disequilibrium_by_variant_data_api_v2_dataset_ldByVariant_get), no default value is provided in `get_linkage_disequilibrium_by_variant_data()` as providing `NULL` or an unrecognised variant ID returns an empty response.
-  - [ ] Are all documented in `gtexr_arguments.R`. Rules...see also link to separate section(?) (**TO DO**)
-  - [ ] All functions therefore use `@inheritParams gtexr_arguments` for documentation
-
-- [ ] Use `@family` roxygen tag to match categories on API documentation e.g. ... . This is used to categorise functions on pkgdown site reference page.
-- [ ] All return a tibble
-- [ ] The first example in `@examples` must produce output, where possible, and be a single function call without assignment (e.g. `get_news_items()`, not `x <- get_news_items()`). This is used to pre-populate argument values in the gtexr shiny app with a working example.
-- [ ] All examples should be surrounded by `\dontrun{}`.
-- [ ] `gtexr_arguments()` metadata ... (*new section*)
-
-## TODO
-
-- [ ] Complete above documentation
-- [ ] Add unit test(s) to enforce above (e.g. check that URL to )
-
+-   Function name is title of API endpoint in lower case, with words separated by underscores.
+-   `@description` section is copied verbatim from the API documentation site and ends with a link to the corresponding API endpoint documentation.
+-   Further notes may be added under `@details`.
+-   Arguments
+    -   Names match those for API endpoint, except where the argument accepts an array (vector in R) of values, in which case it is pluralised.[^1]
+    -   Default values also match those for API endpoint.
+    -   Query parameters flagged as "required" in the GTEx Portal API documentation do not have default values.[^2]
+    -   Are all documented in `gtexr_arguments.R`. All functions therefore use `@inheritParams gtexr_arguments` for documentation.
+-   Use `@family` roxygen tag to match categories on API documentation. This is used to categorise functions on pkgdown site reference page.
+-   Return a tibble.
+-   The first example in `@examples` must produce output and be a single function call without assignment (e.g. `get_news_items()`, not `x <- get_news_items()`). This is used to pre-populate argument values in the gtexr shiny app with a working example.
+-   All examples should be surrounded by `\dontrun{}`.
+
+[^1]: Note that the [Get Genomic Features](https://gtexportal.org/api/v2/redoc#tag/Reference-Genome-Endpoints/operation/get_genomic_features_api_v2_reference_features__featureId__get) endpoint takes a path parameter "featureId". The corresponding gtexr argument is prefixed with "." (`.featureId`).
+
+[^2]: Note however that while `variantId` is not flagged as "required" for [Get Linkage Disequilibrium By Variant Data](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_linkage_disequilibrium_by_variant_data_api_v2_dataset_ldByVariant_get), no default value is provided in `get_linkage_disequilibrium_by_variant_data()` as providing `NULL` or an unrecognised variant ID returns an empty response.
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,3 +12,4 @@ @@
     ^.vscode$
     ^doc$
     ^Meta$
+    ^cran-comments\.md$