Run gene set analysis with various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
The Piano package consists of two parts. The major part revolves around gene
set analysis (GSA), and the central function for this is
runGSA. There are some downstream functions (e.g.
geneSetSummary) that handle
the results from the GSA. By running
runGSA multiple times with
different settings it is possible to compute consensus gene set scores.
Another set of functions (e.g.
consensusHeatmap) take a list of result objects given by
runGSA for this step. The second part of the Piano package contains a
set of functions devoted for an easy-to-use approach on microarray analysis
(wrapped around the affy and limma
packages), which are constructed to integrate nicely with the downstream GSA
part. The starting function in this case is
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