gsea.filter: Take a GSEA list, and filter out genesets that fail various...

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

Description

The criteria are additive.

Usage

gsea.filter(x, N = NULL, NES = NULL, FDR = NULL, P = NULL,
  FWER = NULL, direction = NULL, genesets = NULL)

Arguments

x	a gsea list
N	keep the top 'N' genesets, eg 50
NES	keep the genesets with |NES| > |NES threshold|.
FDR	keep the genesets with NOM.p.val, FDR.q.val or FWER.p.val < threshold
P	keep the genesets with NOM.p.val, FDR.q.val or FWER.p.val < threshold
FWER	keep the genesets with NOM.p.val, FDR.q.val or FWER.p.val < threshold
direction	"up", "down", or NULL or "either"
genesets	a vector of geneset ID's such that only these genesets will be retained.

Value

a GSEA list with probably fewer genesets in the top table, the leading edge list, and the edb object [if present]. also, a filter.settings list is added which details which settings were used

Author(s)

Mark Cowley, 2009-09-03

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