GeneGeneInteR

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeneGeneInteR.

Tools for Testing Gene-Gene Interaction at the Gene Level

Bioconductor version: 3.8

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 (version "3.5") and enter:


if (!require("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")

GeneGeneInteR Introduction PDF R Script

Pairwise interaction tests PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Genetics, GenomeWideAssociation, SNP, Software

Version 1.8.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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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Package Archives

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

Source Package GeneGeneInteR_1.8.0.tar.gz

Windows Binary GeneGeneInteR_1.8.0.zip

Mac OS X 10.11 (El Capitan) GeneGeneInteR_1.8.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/GeneGeneInteR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneGeneInteR

Bioc Package Browser https://code.bioconductor.org/browse/GeneGeneInteR/

Package Short Url https://bioconductor.org/packages/GeneGeneInteR/

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Old Source Packages for BioC 3.8 Source Archive