update get_linkage_disequilibrium_*() functions and add test for shar…

…ed utility function

R/get_linkage_disequilibrium_by_variant_data.R

@@ -1,20 +1,21 @@
-#'Get Linkage Disequilibrium By Variant Data
+#' Get Linkage Disequilibrium By Variant Data
 #'
-#'@description
-#' - Find linkage disequilibrium (LD) data for a given variant
+#' @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 Datasets Endpoints
+#' @inheritParams gtexr_arguments
+#' @return A tibble.
+#' @export
+#' @family Datasets Endpoints
 #'
 #' @examples
-#' get_linkage_disequilibrium_by_variant_data()
-get_linkage_disequilibrium_by_variant_data <- function(variantId = NULL,
-                                                      page = 0,
-                                                      itemsPerPage = 250){
-  gtex_query(endpoint = "dataset/ldByVariant")
+#' get_linkage_disequilibrium_by_variant_data("chr1_159245536_C_T_b38")
+get_linkage_disequilibrium_by_variant_data <- function(variantId,
+                                                       page = 0,
+                                                       itemsPerPage = 250) {
+  resp_body <- gtex_query(endpoint = "dataset/ldByVariant", return_raw = TRUE)
+
+  process_resp_body_linkage_disequilibrium(resp_body)
 }

R/get_linkage_disequilibrium_data.R

@@ -20,18 +20,8 @@
 get_linkage_disequilibrium_data <- function(gencodeId,
                                             datasetId = "gtex_v8",
                                             page = 0,
-                                            itemsPerPage = 250){
-  result <- gtex_query(endpoint = "dataset/ld",
-             return_raw = TRUE)
+                                            itemsPerPage = 250) {
+  resp_body <- gtex_query(endpoint = "dataset/ld", return_raw = TRUE)
 
-  paging_info_messages(result)
-
-  result$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")
-    )
+  process_resp_body_linkage_disequilibrium(resp_body)
 }

R/utils.R

@@ -0,0 +1,17 @@
+process_resp_body_linkage_disequilibrium <- function(resp_body) {
+  paging_info_messages(resp_body)
+
+  if (rlang::is_empty(resp_body$data)) {
+    return(tibble::tibble())
+  }
+
+  resp_body$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")
+    ) |>
+    dplyr::mutate("ld" = as.numeric(.data[["ld"]]))
+}

tests/testthat/test-utils.R

@@ -0,0 +1,39 @@
+test_that(
+  "`process_resp_body_linkage_disequilibrium()` handles both valid and empty responses",
+  {
+    # empty response
+    expect_equal(process_resp_body_linkage_disequilibrium(list(
+      data = list(),
+      paging_info = list(
+        numberOfPages = 0,
+        page = 0,
+        maxItemsPerPage = 250,
+        totalNumberOfItems = 0
+      )
+    )),
+    tibble::tibble())
+
+    # valid response (`get_linkage_disequilibrium_by_variant_data("chr1_153209639_T_C_b38")`)
+    expect_equal(
+      process_resp_body_linkage_disequilibrium(list(
+        data = list(
+          list(
+            "chr1_153202482_C_T_b38,chr1_153209639_T_C_b38",
+            "0.28083400000000003"
+          )
+        ),
+        paging_info = list(
+          numberOfPages = 1,
+          page = 0,
+          maxItemsPerPage = 250,
+          totalNumberOfItems = 162
+        )
+      )),
+      tibble::tibble(
+        variantId_1 = "chr1_153202482_C_T_b38",
+        variantId_2 = "chr1_153209639_T_C_b38",
+        ld = 0.28083400000000003 # should be numeric
+      )
+    )
+  }
+)

vignettes/developer_guide.Rmd

@@ -30,6 +30,7 @@ library(gtexr)
   - [ ] 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