Description Usage Arguments Value Author(s)
View source: R/export.gsea.leadingedge.analysis.R
Export the plots and tables required for a GSEA leading edge analysis.
1 | export.gsea.leadingedge.analysis(x, dir, prefix = NULL, sep = "-")
|
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 |
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.
Mark Cowley, 2009-10-29
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