GeneGeneInteR

DOI: 10.18129/B9.bioc.GeneGeneInteR    

Tools for Testing Gene-Gene Interaction at the Gene Level

Bioconductor version: Release (3.6)

The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results.

Author: Mathieu Emily, Nicolas Sounac, Florian Kroell, Magalie Houee-Bigot

Maintainer: Mathieu Emily <mathieu.emily at agrocampus-ouest.fr>, Magalie Houee-Bigot <magalie.houee at agrocampus-ouest.fr>

Citation (from within R, enter citation("GeneGeneInteR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GeneGeneInteR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GeneGeneInteR")

 

PDF R Script GeneGeneInteR Introduction
PDF R Script Pairwise interaction tests
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneticVariability, Genetics, GenomeWideAssociation, SNP, Software
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.3)
Imports snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table, rioja, grDevices, graphics, stats, utils
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GeneGeneInteR_1.4.0.tar.gz
Windows Binary GeneGeneInteR_1.4.0.zip
Mac OS X 10.11 (El Capitan) GeneGeneInteR_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneGeneInteR
Package Short Url http://bioconductor.org/packages/GeneGeneInteR/
Package Downloads Report Download Stats

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