R/get_tissue_site_detail.R

In gtexr: Query the GTEx Portal API

#' Get Tissue Site Detail
#'
#' @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)
#'
#' @inheritParams gtexr_arguments
#' @returns A tibble. Or a list if `.return_raw = TRUE`.
#' @export
#' @family Datasets Endpoints
#'
#' @examples
#' \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(datasetId = "gtex_v8",
                                   page = 0,
                                   itemsPerPage = getOption("gtexr.itemsPerPage"),
                                   .verbose = getOption("gtexr.verbose"),
                                   .return_raw = FALSE) {
  gtex_query(endpoint = "dataset/tissueSiteDetail", process_get_tissue_site_detail_resp_json)
}

process_get_tissue_site_detail_resp_json <- function(resp_json) {
  resp_json$data |>
    purrr::map(\(x) purrr::map_if(x, is.list, \(y) list(y))) |>
    dplyr::bind_rows()
}