R/clinicalData.R

In acidgenomics/cBioPortalAnalysis: cBioPortal Analysis Utilities

#' Get available clinical data for samples in a case list
#'
#' @export
#' @note Updated 2022-06-06.
#'
#' @inheritParams params
#'
#' @seealso
#' - `caseLists()`.
#' - `cancerStudies()`.
#'
#' @return `DataFrame`.
#'
#' @examples
#' ## DLBCL TCGA ====
#' x <- clinicalData(caseList = "dlbc_tcga_pan_can_atlas_2018_rna_seq_v2_mrna")
#' print(x)
#'
#' ## CCLE Broad 2019 ====
#' x <- clinicalData(caseList = "ccle_broad_2019_sequenced")
#' print(x)
clinicalData <- function(caseList) {
    assert(isString(caseList))
    x <- tryCatch(
        expr = {
            getClinicalData(x = .cgds(), caseList = caseList)
        },
        error = function(e) {
            ## This currently happens for "ccle_broad_2019_all", for example.
            abort(sprintf(
                "{.pkg %s} query failure for {.var %s}.",
                "cgdsr", caseList
            ))
        }
    )
    assert(
        is.data.frame(x),
        hasNoDuplicates(rownames(x))
    )
    rownames(x) <- makeNames(rownames(x))
    colnames(x) <- camelCase(colnames(x), strict = TRUE)
    x <- sanitizeNA(x)
    x <- as(x, "DataFrame")
    x <- x[sort(rownames(x)), sort(colnames(x))]
    x
}