plot_gsea.leadingedge.heatmap.auto: Generate a heatmap of genesets from a GSEA run, across a...

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

Description

Generate a heatmap of genesets from a GSEA run, across a number of standard thresholds The default settings will generate 4 heatmaps, of the up/down, top 50, and FDR<0.25 genesets.

Usage

plot_gsea.leadingedge.heatmap.auto(x, file = NULL, N = c(50),
  FDR = c(0.25), P = NULL, FWER = NULL, pdf.width = 12,
  pdf.height = 12)

Arguments

x	a GSEA obect
file	the path to a PDF file, or NULL to use dev.cur
N	an integer vector of thresholds on the top N genesets, sorted by |NES|
FDR	an integer vector of FDR thresholds
P	an integer vector of unadjusted P-value thresholds
FWER	an integer vector of FWER thresholds
pdf.width	the width of the pdf device in inches
pdf.height	the height of the pdf device in inches

Value

nothing. creates a pdf file.

Author(s)

Mark Cowley, 2010-10-14

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