R/gsea.convert.clm2cls.R

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

#' Convert a clm file into a cls file.
#' 
#' @param clm.file the path to a clm file
#' @param cls.file if NULL, the cls file will be in the same dir as the clm,
#'   and will have the suffix cls.
#' 
#' @return invisibly return a cls file name
#' 
#' @author Mark Cowley, 2009-12-21
#' @export
gsea.convert.clm2cls <- function(clm.file, cls.file=NULL) {
	if( is.null(cls.file)) 
		cls.file <- sub("clm", "cls", clm.file)
		
	tmp <- import.gsea.clm(clm.file)
	export.broad.cls(tmp[,3], cls.file, continuous=FALSE)
	
	invisible(cls.file)
}