R/utils.R

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

#' Extract gene-set namespace from RONET GMT files
#' @param gmtList A \code{GmtList} object read from a RONET GMT file
#' @return Character vector of the same length, indicating categorie
#' @importFrom BioQC gsDesc
#' @export
ronetGeneSetNamespace <- function(gmtList) {
  sapply(strsplit(BioQC::gsDesc(gmtList), "\\|"), "[[", 1L)
}

#' Read RONET GMT files with namespace information
#' @param file A GMT file in the RONET format, where in the 'desc' field a namespace is appended at the beginning, separated from the rest of the description with a pipe
#' @return A \code{GmtList} object with an additional 'namespace' item in each list
#' @export
readRonetGmt <- function(file) {
  resRaw <- BioQC::readGmt(file)
  res <- new("GmtList")
  res@.Data <- lapply(resRaw, function(x) {
    splitDesc <- strsplit(x$desc, "\\|")[[1]]
    x$namespace <- splitDesc[[1]]
    x$desc <- paste(splitDesc[-1], collapse="|")
    return(x)
  })
  names(res) <- names(resRaw)
  return(res)
}

#' Return the size (unique length) of gene-sets
#' @param gmtList a \code{GmtList} object
#' @return An integer vector
#' @export
gsSize <- function(gmtList) {
   sapply(gsGenes(gmtList), ribiosUtils::ulen)
}

#' Print contributing genes
#' @param geneLabels A vector of character strings
#' @param geneValues A vector of numeric values
#' @return A vector of character strings
#' @export
printContributingGenes <- function(geneLabels, geneValues) {
  paste(sprintf("%s(%1.2f)",
                geneLabels, geneValues), collapse=",")
}