#' Function for getting available TCGA cancer disease codes
#'
#' A convenience function to get available cancer codes from TCGA. It excludes
#' joint codes such as `COADREAD` and `GBMLGG`, among others. See the
#' `diseaseCodes` datasets in `TCGAutils` for a complete list.
#'
#' @return A vector of named disease codes
#' @export
getDiseaseCodes <- function() {
nev <- new.env()
data("diseaseCodes", package = "TCGAutils", envir = nev)
diseaseCodes <- nev[["diseaseCodes"]]
excludedCodes <- c("COADREAD", "GBMLGG", "KIPAN",
"STES", "FPPP", "CNTL", "LCML", "MISC")
logicalSub <- !diseaseCodes[[1L]] %in% excludedCodes
diseases <- diseaseCodes[logicalSub, "Study.Abbreviation"]
setNames(diseases, diseases)
}
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