gsea.rename.genesets.edb: Parse an edb XML object, and rename the genesets with...

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

Description

This is intended to be used by gsea.rename.genesets, which should calculate old.names and new.names. Entries in edb, given that they are xml are in no strict order (although they seem to be ordered from most -ve NES to most +ve NES). Thus you need to supply the old.names is so that we can ensure the entries in edb get renamed correctly.

Usage

gsea.rename.genesets.edb(edb, old.names, new.names)

Arguments

edb	an XMLDocument. See import.gsea.edb(..., edb=TRUE)
old.names	a vector of original geneset names. these should be found within the edb names
new.names	the new names, in the same order as the old names.

Value

An mutable XMLInternalDOM (ie an XML tree much like an XMLDocument but which can be modified) which is a copy of the original edb XMLDocument.

Author(s)

Mark Cowley, 2009-10-06

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