R/calculate_isqtls.R

In gtexr: Query the GTEx Portal API

#' Calculate Isqtls
#'
#' @description Calculate your own Cell Specific sQTLs.
#'
#' - This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.
#' - This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.
#'
#' By default, the calculation is based on the latest GTEx release.
#'
#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_ieqtls_api_v2_association_dynieqtl_get).
#'
#' @inheritParams gtexr_arguments
#'
#' @return A tibble.
#' @export
#' @family Dynamic Association Endpoints
#'
#' @examples
#' \dontrun{
#' # perform request
#' calculate_isqtls(cellType = "Neutrophils",
#'                  tissueSiteDetailId = "Whole_Blood",
#'                  phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
#'                  variantId = "chr1_1099341_T_C_b38")
#' }
calculate_isqtls <-
  function(cellType,
           tissueSiteDetailId,
           phenotypeId,
           variantId,
           datasetId = "gtex_v8") {
    gtex_query(endpoint = "association/dynisqtl", return_raw = TRUE) |>
      purrr::imap(\(x, idx) ifelse(is.list(x),
                                   tibble::tibble(
                                     data = purrr::map_depth(x,
                                                             purrr::pluck_depth(x) - 2,
                                                             unlist)
                                   ),
                                   x)) |>
      tibble::as_tibble()
  }