GeneGeneInteR

DOI: 10.18129/B9.bioc.GeneGeneInteR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GeneGeneInteR.

Tools for Testing Gene-Gene Interaction at the Gene Level

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GeneGeneInteR")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	GPL (>= 2)
Depends	R (>= 3.5)
Imports	snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table, grDevices, graphics, stats, utils, methods
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Package Archives

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

Source Package	GeneGeneInteR_1.10.0.tar.gz
Windows Binary	GeneGeneInteR_1.10.0.zip
Mac OS X 10.11 (El Capitan)	GeneGeneInteR_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GeneGeneInteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GeneGeneInteR
Package Short Url	https://bioconductor.org/packages/GeneGeneInteR/
Package Downloads Report	Download Stats