R/aveytoolkit_writeGMT.R

In stefanavey/aveytoolkit: Toolkit of Helper Functions

##' aveytoolkit_writeGMT.R
##' 
##' Write out a GMT (Gene Matrix Transposed) file.
##' 
##' @author Stefan Avey
##' @details Take in a vector of set names, descriptions, and gene identifiers and
##'          write them to a GMT file format.
##'          http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
##' @param filename the file to write to (should include '.gmt' extension
##' @param sets a list of character vectors containing the sets to write
##' @param setNames a character vector of set names corresponding to sets.
##'        Defaults to 1, 2, 3, ..., length(sets) if nonte specified.
##' @param setDescriptions a character vector of set descriptions corresponding
##'        to sets. Defaults to \code{NA} values if none specified.
##' @export
writeGMT <- function(filename, sets, setNames = names(sets),
                     setDescriptions = rep(NA, length(sets))) {
  lines <- vector(mode = "character", length=length(sets))
  if(length(sets) != length(setNames)) {
    stop("`setNames` and `sets` must be the same length")
  }
  if(length(sets) != length(setDescriptions)) {
    stop("`setDescriptions` and `sets` must be the same length")
  }
  for(i in seq_along(sets)) {
    lines[i] <- paste(setNames[i], setDescriptions[i],
                       paste0(sets[[i]], collapse = '\t'), sep='\t')
  }
  write(lines, file = filename, sep = '\n')
}