gsea.combine: Combine N gsea runs together

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

Description

This merges N independent GSEA results into a single much larger GSEA result object. So that you don't end up with N copies of each geneset, you need to rename the genesets before running this code to uniquify them, eg adding a short prefix tag (eg “MCF7” or “T47D”) is enough to uniquify the geneset names. You should probably also run some sort of geneset filtering, to keep the result size manageble, and since filtering on this combined list may fail.

Usage

gsea.combine(..., gsea.runs, verbose = TRUE)

Arguments

gsea.runs	a list of GSEA objects. This overrides ...
verbose	logical.
...	at least 2 individual GSEA objects, or

Value

a GSEA object with larger tt, and larger leading.edge objects. Currently, the rnk and edb objects are set to NA – WARNING: this may make routines that work on GSEA objects fail. We recommend treating results from gsea.combine as immutable objects.

TODO

delete the gsea.runs param; users can just use call("gsea.combine", my.gsea.list)

Author(s)

Mark Cowley, 2010-08-16

See Also

gsea.rename.genesets gsea.filter

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