export.gsea.leadingedge.analysis: Export the plots and tables required for a GSEA leading edge...

Description Usage Arguments Value Author(s)

View source: R/export.gsea.leadingedge.analysis.R

Description

Export the plots and tables required for a GSEA leading edge analysis.

Usage

1
export.gsea.leadingedge.analysis(x, dir, prefix = NULL, sep = "-")

Arguments

x

a GSEA object. Usually this will have been heavily subset to genesets of interest. eg using gsea.split, or gsea.filter(..., gensets=<>)

dir

the directory where files will be made.

prefix

an optional prefix to differentiate these files from others that you might make. eg WTvsKO1

sep

the seperator to use in constructing the outputfilename. Ignored if prefix=NULL

Value

Creates N files:
leadingedge.plots.pdf: 4 plots in a single PDF file
leadingedge.genes.txt: simple text format of genesymbols. useful for GO analysis (using eg DAVID)
leadingedge.genecounts.xls: a 2 column table of genes with their counts in the N genesets
leadingedge.adjmat.xls: a genes x genesets adjacency matrix.
leadingedge.tree.cdt: a fileformat that lets you view the hierarchical clustering of genesets using the HierarchicalClusteringViewer tool @ Broad's GenePattern.
leadingedge.tree.gtr: used in conjunction with the cdt file.

Author(s)

Mark Cowley, 2009-10-29


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