RTopper-package: A package to perform run Gene Set Enrichment across genomic...

In RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

Description

Gene sets analysis considers whether genes sharing a biological property also behave in a related way in experimental data. This technique is commonly used in high throughput genomic analyses to assist results interpretation, and has been successfully applied in cancer genome projects for integrating information from multiple genome-wide assays. The RTopper package uses gene sets analysis to overcome the diversity of genomic data providing the statistical framework for integration across data types.

Details

Package:	RTopper
Type:	Package
Version:	0.1
Date:	2010-11-12
License:	GPL version 3 or newer

RTopper package features

Rtopper enables two gene set-based data integration approaches:

1

Integration+GSA: computing integrated gene-to-phenotype association scores, followed by conventional gene sets analysis;

2

GSA+Integration: computing consensus significance score after all data types are analyzed individually;

3

Use of alternative enrichment test: RTopper uses the Wilcoxon rank-sum test for enrichment testing, however alternative tests can be defined and used;

4

Multiple testing correction: RTopper enables adjustment of p-values obtained from enrichment analysis;

Author(s)

Luigi Marchionni [e-mail]

References

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, and Giovanni Parmigiani. "Integrating diverse genomic data using gene sets." Manuscript submitted.

RTopper documentation built on Nov. 8, 2020, 5:08 p.m.