R/prepareGeneSetFiles.R

In steinbaugh/pfgsea: Acid Genomics GSEA

#' Prepare gene set files
#'
#' @details
#' Intended primarily to match GMT files from MSigDb.
#'
#' @note Updated 2021-10-20.
#' @export
#'
#' @inheritParams params
#'
#' @param dir `character(1)`.
#' Directory name containing MSigDb release.
#'
#' @param ext `character(1)`.
#' Gene set file extension.
#' Case insensitive.
#'
#' @param recursive `logical(1)`.
#' Whether to search for gene set files recursively in `dir` argument.
#'
#' @seealso
#' - https://www.gsea-msigdb.org/gsea/msigdb/
#' - https://www.ncbi.nlm.nih.gov/gene/
#'
#' @examples
#' dir <- system.file(
#'     "extdata",
#'     "msigdb",
#'     "7.0",
#'     "msigdb_v7.0_GMTs",
#'     package = "AcidGSEA",
#'     mustWork = TRUE
#' )
#' files <- prepareGeneSetFiles(dir, keyType = "geneName")
#' print(files)
prepareGeneSetFiles <-
    function(dir,
             keyType = c("geneName", "ncbiGeneId"),
             ext = "gmt",
             recursive = FALSE) {
        assert(
            isADir(dir),
            isString(ext),
            isFlag(recursive)
        )
        keyType <- match.arg(keyType)
        keyType2 <- switch(
            EXPR = keyType,
            "ncbiGeneId" = "entrez",
            "geneName" = "symbols"
        )
        dir <- realpath(dir)
        files <- sort(list.files(
            path = dir,
            pattern = paste0("*.", keyType2, "\\.", ext, "$"),
            full.names = TRUE,
            recursive = recursive,
            ignore.case = TRUE
        ))
        assert(
            hasLength(files),
            msg = sprintf(
                "Failed to detect any gene sets in {.dir %s}.",
                dir
            )
        )
        files <- realpath(files)
        alertInfo(sprintf(
            "Detected %d %s %s of {.var %s} {.val %s} in {.path %s}.",
            length(files),
            toupper(ext),
            ngettext(
                n = length(files),
                msg1 = "file",
                msg2 = "files"
            ),
            "keyType", keyType,
            dir
        ))
        names(files) <- snakeCase(basenameSansExt(files))
        files
    }