gsea.genesets2gct: Create gct files for all gseaPreranked runs comparing 1 rnk...

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

Description

By default, the leading edge genes are identified by the leading.edge slot from running import.gsea(); this then creates an edb/leading_edge.gmt file. From a gct.file at the unique genesymbol level (see gsea.gct.probes2genes), the relevant rows are retrieved, keeping the same order as the genes in the leading edge itself.

Usage

gsea.genesets2gct(gsea.dir, gct.file, leading.edge = TRUE,
  which.sets = c("best", "all"))

Arguments

gsea.dir	either a single gsea directory, or a parent-dir that contains lots of gsea dirs, (each vs a different collection of genesets)
gct.file	a unique gene-level gct file (very important to see gsea.gct.probes2genes)
leading.edge	if TRUE then only the leading edge genes are exported, or else, the genes in the same order as given by edb/gene_sets.gmt are given.
which.sets	do you want to make a gct for every single leading edge ("all"), or just those that have been created in the dir ("best") which are usually the top 20 or 50.

Value

Undocumented return value

Author(s)

Mark Cowley, 2009-07-27

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