R/gsea.hardwire.rpt.paths.R

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

#' Rewire the file locations referenced within a GSEA rpt file.
#' 
#' Why? If you run a GSEA on a GenePattern server, you can end up with files
#' in a rpt file that you can
#' no longer access on the machine where you're analysing the GSEA results...
#' Useful if you have a directory full of chip files, and gmx files.
#' 
#' @param dir a GSA directory. The rpt file within this dir will be modified.
#' @param chip.dir the directory containing your GSEA .chip files
#' @param gmx.dir the directory containing your GSEA .gmx/.gmt files
#' @return none. the rpt file will be modified.
#' @author Mark Cowley, 2009-12-11
#' @export
gsea.hardwire.rpt.paths <- function(dir, chip.dir="/pwbc/data/GSEA/chips", gmx.dir="/pwbc/data/GSEA/gmt/v2.5") {
	rpt <- import.gsea.rpt(dir)
	rpt$chip <- file.path(chip.dir, basename(rpt$chip))
	rpt$gmx <- file.path(gmx.dir, basename(rpt$gmx))
	rpt.name <- dir(dir, pattern=".*\\.rpt", full.names=TRUE)

	export.gsea.rpt(rpt, rpt.name)
}