piano-package {piano} | R Documentation

## Piano - Platform for Integrative ANalysis of Omics data

### Description

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.

### Details

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. `GSAsummaryTable` and `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. `consensusScores` and `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 `loadMAdata`.

### Author(s)

Leif Varemo piano.rpkg@gmail.com and Intawat Nookaew piano.rpkg@gmail.com

### See Also

`runGSA` and `loadMAdata`

[Package piano version 2.0.2 Index]