R/Genesets-geneSetsFromFile.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' Creates a GeneSetCollection object from a file
#'
#' \code{geneSetsFromFile} creates a GeneSetCollection object from the data
#' present in a file. The file must be a tab separated values file (tsv). Each
#' line will parse to a GeneSet. First field will be the GeneSet setName, the
#' second the setIdentifier and the remaining are the genes.
#'
#' @param filePath character with the path of the file to parse.
#' @param is_GO logical indicating if this gene sets are from the Gene Ontology.
#' If true, then each gene GeneSet setName must be a GO id.
#' @param ... not in use.
#'
#' @return A GeneSetCollection object.
#'
#' @docType methods
#' @name geneSetsFromFile
#' @rdname Genesets-geneSetsFromFile
#' @seealso \code{\link{as.Genesets}}
#' @seealso \code{\link{Genesets-enrichr}}
#' @seealso \code{\link{loadGo}}
#'
#' @exportMethod geneSetsFromFile
#' @examples
#' ## Create some fake gene sets in a data.frame to save them in disk and then
#' ## load them (10 gene sets with 20 genes each (it is not neccesary that they
#' ## have the same number of genes).
#' gsets <- data.frame(
#'   IDs = paste("set", 1:10),
#'   Names = rep("", 10),
#'   matrix(paste("gene", 1:(10 * 20)), nrow = 10)
#' )
#' ## And save this file as a tab separated file.
#' geneSetsFile <- paste(tempdir(), "/fakeGsets.tsv", sep = "")
#' write.table(gsets,
#'   file = geneSetsFile, sep = "\t",
#'   col.names = FALSE, row.names = FALSE, quote = FALSE
#' )
#' ## Now lets load this tsv file as a GeneSetCollection object.
#' myGsets <- geneSetsFromFile(geneSetsFile)
#' ## And lets delete this tsv file (so we dont have garbage in our disk).
#' unlink(geneSetsFile)
setGeneric(name = "geneSetsFromFile", def = function(filePath, ...) {
  standardGeneric("geneSetsFromFile")
})

#' @rdname Genesets-geneSetsFromFile
#' @aliases geneSetsFromFile,character-method
#'
#' @importFrom futile.logger flog.error
setMethod(
  f = "geneSetsFromFile",
  signature = c("character"),
  definition = function(filePath, is_GO = FALSE) {
    stopifnot(length(filePath) == 1)

    # check if file exists, its not a directory, its readable
    if (!file.exists(filePath) || dir.exists(filePath)
    || (file.access(filePath, 4) == -1)) {
      flog.error("Gene sets file path error, check if it is readable.")
    }

    collection <- NullCollection()
    if (is_GO) {
      collection <- GOCollection()
    }

    tmp <- readLines(filePath)
    gsets <- lapply(tmp, function(actLine) {
      # for each line, fst item is id, snd is name, rest are genes
      t <- strsplit(actLine, "\t")[[1]]

      actId <- t[[1]]
      actName <- t[[2]]
      if (actName == "") {
        actName <- actId
      }

      actGS <- GeneSet(unique(t[3:length(t)]),
        setIdentifier = actName,
        setName = actId, collectionType = collection
      )
      return(actGS)
    })

    return(GeneSetCollection(gsets))
  }
)