GeneGeneInteR

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see GeneGeneInteR.

Tools for Testing Gene-Gene Interaction at the Gene Level


Bioconductor version: 3.10

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 "3.6") 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

Details

biocViews GeneticVariability, Genetics, GenomeWideAssociation, SNP, Software
Version 1.12.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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_1.12.0.tar.gz
Windows Binary GeneGeneInteR_1.12.0.zip
Mac OS X 10.11 (El Capitan) GeneGeneInteR_1.12.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive