update get_gene_expression()

R/get_gene_expression.R

@@ -1,29 +1,58 @@
 #' Get Gene Expression
 #'
-#' @description
-#' - Find normalized gene expression data.
+#' @description Find normalized gene expression data.
+#'
 #' - Returns normalized gene expression in tissues at the sample level.
 #' - Results may be filtered by dataset, gene or tissue, but at least one gene must be provided.
-#' - By default, this service queries the latest GTEx release.
 #'
-#'[GTEx Portal API
-#'documentation](https://gtexportal.org/api/v2/redoc#tag/Expression-Data-Endpoints/operation/get_gene_expression_api_v2_expression_geneExpression_get)
+#' By default, this service queries the latest GTEx release.
+#'
+#'  [GTEx Portal API
+#'   documentation](https://gtexportal.org/api/v2/redoc#tag/Expression-Data-Endpoints/operation/get_gene_expression_api_v2_expression_geneExpression_get)
 #'
 #' @inheritParams gtexr_arguments
 #'
-#' @return A Tibble
+#' @return A tibble.
 #' @export
 #' @family Expression Data Endpoints
 #'
 #' @examples
 #' \dontrun{
-#' get_gene_expression(gencodeIds = "ENSG00000132693.12")
+#'   # multiple genes, selected tissues
+#'   get_gene_expression(gencodeIds = c("ENSG00000132693.12",
+#'                                      "ENSG00000203782.5"),
+#'                       tissueSiteDetailIds = c("Thyroid", "Whole_Blood"))
+#'
+#'   # single gene, selected (single) tissue
+#'   get_gene_expression(gencodeIds = "ENSG00000132693.12",
+#'                       tissueSiteDetailIds = "Whole_Blood")
+#'
+#'   # subset by sex
+#'   get_gene_expression(gencodeIds = "ENSG00000132693.12",
+#'                       tissueSiteDetailIds = "Whole_Blood",
+#'                       attributeSubset = "sex")
+#'
+#'   # subset by age bracket
+#'   get_gene_expression(gencodeIds = "ENSG00000132693.12",
+#'                       tissueSiteDetailIds = "Whole_Blood",
+#'                       attributeSubset = "ageBracket")
 #' }
 get_gene_expression <- function(gencodeIds,
                                 datasetId = "gtex_v8",
-                                tissueSiteDetailId = NULL,
+                                tissueSiteDetailIds = NULL,
                                 attributeSubset = NULL,
                                 page = 0,
-                                itemsPerPage = 250){
-  gtex_query(endpoint = "expression/geneExpression")
+                                itemsPerPage = 250) {
+  resp_body <- gtex_query(endpoint = "expression/geneExpression", return_raw = TRUE)
+
+  paging_info_messages(resp_body)
+
+  resp_body$data |>
+    purrr::map(\(x) {
+      x$data <- list(as.numeric(x$data))
+      x |>
+        purrr::map_if(is.null, \(y) NA) |>
+        tibble::as_tibble()
+    }) |>
+    dplyr::bind_rows()
 }