R/gsea.reorder.gmt.by.rnk.R

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

#' Reorder the genes within a gmt object to match the order of genes within a
#' rnk object
#' 
#' @param gmt a gmt object (ie a named list of genes)
#' @param rnk a rnk object (ie named list of gene scores, where genes are the
#'   names)
#' 
#' @return a gmt just like input, but with the genes reordered to match the
#'   order inside the rnk
#' 
#' @author Mark Cowley, 2009-12-07
#' @export
gsea.reorder.gmt.by.rnk <- function(gmt, rnk) {
	N <- length(gmt)
	rnk <- rnk[order(rnk, decreasing=TRUE)]
	rnk <- names(rnk)
	
	for(i in 1:N) {
		gmt[[i]] <- rnk[ rnk %in% gmt[[i]] ]
	}

	return( gmt )
}