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

Description Usage Arguments Details Value Author(s) References See Also

cdt files = Clustered Data Table; gtr files = gene tree file. These files describe the ordering of usually a matrix of gene expression data, however we have used this notation to represent the relationships between GSEA leading edge genesets. You can view these files using the HierarchicalClusteringViewer tool in GenePattern.

1	export.gsea.cdt(x, file, gtr = TRUE, rename = FALSE)

`x`	a gsea object (not the leading.edge)
`file`	the path to a cdt file. This should have the .cdt extension
`gtr`	if TRUE, then a gtr file will also be made. It gets its filename from the cdt. if `FALSE`, then it will not be made (can't see why that would be useful to you though?)
`rename`	logical: rename the genesets to at most 40 characters? see `gsea.rename.genesets`
`...`	Unprocessed arguments for export.gsea.gtr.

The order of the tree should be identical to plot_gsea.leadingedge.HCL, so you could compare a static pdf image (from plot_gsea.leadingedge.HCL), or interrogate a dynamically updating image using the GenePattern tool.

nothing. Creates a cdt file, and optionally a gtr file.

Mark Cowley, 2009-10-12

Stanford File formats: http://smd.stanford.edu/help/formats.shtml GenePattern file formats: http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_fileformats.html

plot_gsea.leadingedge.HCL

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