#' Import the output produced by gsea.compare.runs.sh
#'
#' @param xls an XLS file produced by running import.gsea.compare.runs.sh, or
#' import.gsea.compare.runs.1gmt.sh
#' @param gmt either an integer indicating which sheet of the xls to import,
#' or the name of the gmt file. use the latter if gsea was run on all 15 of
#' the gmt categories listed in .GSEA.GMT.CATEGORIES
#' @author Mark Cowley, 2009-03-23
#' @examples
#' \dontrun{
#' gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls")
#' gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", c("c2_all"))
#' gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", c("c2_all", "c5_bp"))
#' gseacmp <- import.gsea.compare.runs("GSEA/gsea.compare.runs.xls", grep("all", .GSEA.GMT.CATEGORIES, value=TRUE))
#' }
#' @export
import.gsea.compare.runs <- function(xls, gmt=.GSEA.GMT.CATEGORIES) {
if( is.null(gmt) )
gmt <- .GSEA.GMT.CATEGORIES
if( length(gmt) > 1 ) {
res <- list()
for(gmt in .GSEA.GMT.CATEGORIES) {
res[[gmt]] <- import.gsea.compare.runs(xls, gmt)
}
return( res )
}
else {
if( is.character(gmt) )
gmt <- match(gmt, .GSEA.GMT.CATEGORIES)
res <- read.xls(xls, sheet=gmt)
return( res )
}
}
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