plot_gsea.venn: Compare the significant genesets from 2 or 3 GSEA runs using...

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

Description

Compare the significant genesets from 2 or 3 GSEA runs using Venn diagrams

Usage

plot_gsea.venn(..., gsea.list = NULL, names = NULL, main = "", N = NULL,
  NES = NULL, FDR = NULL, P = NULL, FWER = NULL,
  direction = c("either", "up", "down"))

Arguments

gsea.list	either 2 or 3 GSEA objects by name, or as elements of gsea.list
names	a character vector of names, 1 per GSEA run
main	plot title prefix, eg "Venn"
N	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
NES	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
FDR	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
P	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
FWER	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
direction	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
...	either 2 or 3 GSEA objects by name, or as elements of gsea.list

Value

a 2D or 3D venn diagram

Author(s)

Mark Cowley, 2010-10-15

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