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

Description Usage Arguments Value Author(s)

View source: R/gsea.filter.R

Description

The criteria are additive.

Usage

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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.