gsea.rename.genesets: Rename the genesets from within a GSEA object.

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

Description

Rename genesets using a prefix and suffix, such that COWLEY_UP becomes: PREFIX_COWLEY_UP_SUFFIX Optionally, the rank, FDR and direction can also be included so that COWLEY_UP becomes: 1: PREFIX_COWLEY_UP_SUFFIX UP (0.002)

Usage

gsea.rename.genesets(x, prefix = NULL, suffix = NULL, fdr = FALSE,
  rank = FALSE, direction = FALSE, maxlen = 60)

Arguments

x	a GSEA list, optionally with an edb. see import.gsea(..., edb=TRUE)
prefix	an optional prefix (such as the treatment, eg WTvsTreatA).
suffix	an optional prefix (such as the treatment, eg WTvsTreatA).
fdr	add the fdr in parentheses to the end? eg " (0.001)"
rank	add the rank at the start? eg "12: "
direction	add UP or DOWN to the end?
maxlen	the max number of characters in the geneset name (before we add rank & fdr & direction to it)

Value

a GSEA list with modified names.

Author(s)

Mark Cowley, 2009-10-14

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