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

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

Description

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

Usage

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.