update get_tissue_site_detail(); updated roxygen2 version - .Rd files…

… updated also
rmgpanw · Jun 21, 2024 · 0109dac · 0109dac
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diff --git a/R/get_tissue_site_detail.R b/R/get_tissue_site_detail.R
@@ -1,19 +1,35 @@
-#'Get Tissue Site Detail
+#' Get Tissue Site Detail
 #'
-#'@description
-#' - Retrieve all tissue site detail information in the database
+#' @description Retrieve all tissue site detail information in the database
 #'
-#'[GTEx Portal API
-#'documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_tissue_site_detail_api_v2_dataset_tissueSiteDetail_get)
+#' [GTEx Portal API
+#' documentation](https://gtexportal.org/api/v2/redoc#tag/Datasets-Endpoints/operation/get_tissue_site_detail_api_v2_dataset_tissueSiteDetail_get)
 #'
-#'@inheritParams gtexr_arguments
-#'@return A Tibble
-#'@export
-#'@family Datasets Endpoints
+#' @inheritParams gtexr_arguments
+#' @return A tibble
+#' @export
+#' @family Datasets Endpoints
 #'
 #' @examples
-#' get_tissue_site_detail()
+#' \dontrun{
+#'   # returns a tibble with one row per tissue
+#'   get_tissue_site_detail()
+#'
+#'   # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns
+#'   bladder_site_details <- get_tissue_site_detail() |>
+#'     dplyr::filter(tissueSiteDetailId == "Bladder")
+#'
+#'   purrr::pluck(bladder_site_details, "eqtlSampleSummary", 1)
+#'
+#'   purrr::pluck(bladder_site_details, "rnaSeqSampleSummary", 1)
+#' }
 get_tissue_site_detail <- function(page = 0,
                                    itemsPerPage = 250){
-  gtex_query(endpoint = "dataset/tissueSiteDetail")
+  result <- gtex_query(endpoint = "dataset/tissueSiteDetail", return_raw = TRUE)
+
+  paging_info_messages(result)
+
+  result$data |>
+    purrr::map(\(x) purrr::map_if(x, is.list, \(y) list(y))) |>
+    dplyr::bind_rows()
 }
diff --git a/man/get_annotation.Rd b/man/get_annotation.Rd
diff --git a/man/get_clustered_median_exon_expression.Rd b/man/get_clustered_median_exon_expression.Rd
diff --git a/man/get_clustered_median_gene_expression.Rd b/man/get_clustered_median_gene_expression.Rd
diff --git a/man/get_clustered_median_junction_expression.Rd b/man/get_clustered_median_junction_expression.Rd
diff --git a/man/get_clustered_median_transcript_expression.Rd b/man/get_clustered_median_transcript_expression.Rd
diff --git a/man/get_collapsed_gene_model_exon.Rd b/man/get_collapsed_gene_model_exon.Rd
diff --git a/man/get_downloads_page_data.Rd b/man/get_downloads_page_data.Rd
diff --git a/man/get_eqtl_genes.Rd b/man/get_eqtl_genes.Rd
diff --git a/man/get_expression_pca.Rd b/man/get_expression_pca.Rd
diff --git a/man/get_file_list.Rd b/man/get_file_list.Rd
diff --git a/man/get_fine_mapping.Rd b/man/get_fine_mapping.Rd
diff --git a/man/get_full_get_collapsed_gene_model_exon.Rd b/man/get_full_get_collapsed_gene_model_exon.Rd
diff --git a/man/get_functional_annotation.Rd b/man/get_functional_annotation.Rd
diff --git a/man/get_gene_expression.Rd b/man/get_gene_expression.Rd
diff --git a/man/get_independent_eqtl.Rd b/man/get_independent_eqtl.Rd
diff --git a/man/get_linkage_disequilibrium_by_variant_data.Rd b/man/get_linkage_disequilibrium_by_variant_data.Rd
diff --git a/man/get_linkage_disequilibrium_data.Rd b/man/get_linkage_disequilibrium_data.Rd
diff --git a/man/get_median_exon_expression.Rd b/man/get_median_exon_expression.Rd
diff --git a/man/get_median_gene_expression.Rd b/man/get_median_gene_expression.Rd
diff --git a/man/get_median_junction_expression.Rd b/man/get_median_junction_expression.Rd
diff --git a/man/get_median_transcript_expression.Rd b/man/get_median_transcript_expression.Rd
diff --git a/man/get_multi_tissue_eqtls.Rd b/man/get_multi_tissue_eqtls.Rd
diff --git a/man/get_sample_datasets_endpoints.Rd b/man/get_sample_datasets_endpoints.Rd
diff --git a/man/get_significant_single_tissue_ieqtls.Rd b/man/get_significant_single_tissue_ieqtls.Rd
diff --git a/man/get_significant_single_tissue_isqtls.Rd b/man/get_significant_single_tissue_isqtls.Rd
diff --git a/man/get_significant_single_tissue_sqtls.Rd b/man/get_significant_single_tissue_sqtls.Rd
diff --git a/man/get_sqtl_genes.Rd b/man/get_sqtl_genes.Rd
diff --git a/man/get_subject.Rd b/man/get_subject.Rd
diff --git a/man/get_tissue_site_detail.Rd b/man/get_tissue_site_detail.Rd
diff --git a/man/get_top_expressed_genes.Rd b/man/get_top_expressed_genes.Rd