gsea.compare.runs.1gmt: Compare N GSEA runs vs a single gmt file (eg lots of rnk...

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

Description

Compare N GSEA runs vs a single gmt file (eg lots of rnk files vs c2_all)

Usage

gsea.compare.runs.1gmt(dirs, gsealist, outfile, method = c("intersect",
  "union")[1])

Arguments

dirs	a vector of gsea directories
gsealist	optional list of gsea runs that you've already imported. over-rides <dirs>
outfile	if specified, an XLS output file will be created.
method	which genesets to keep if they are not the same? “intersect”: just the genesets found in all GSEA runs; “union”: all the genesets found in any GSEA run. NA's will be used for those genesets that were not observed.

Value

a data.frame of “geneset”, “size”, “NES”, “FDR”, “NES”, “FDR”, ...

Author(s)

Mark Cowley, 2009-12-16

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.