GeneGeneInteR

DOI: 10.18129/B9.bioc.GeneGeneInteR    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GeneGeneInteR.

Tools for Testing Gene-Gene Interaction at the Gene Level

Bioconductor version: 3.12

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 [aut, cre], Nicolas Sounac [ctb], Florian Kroell [ctb], Magalie Houee-Bigot [aut]

Maintainer: Mathieu Emily <mathieu.emily at agrocampus-ouest.fr>

Installation

To install this package, start R (version "4.0") 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	1.16.0
In Bioconductor since	BioC 3.4 (R-3.3) (4.5 years)
License	GPL (>= 2)
Depends	R (>= 4.0)
Imports	snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table, grDevices, graphics, stats, utils, methods, GGtools
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GeneGeneInteR_1.16.0.tar.gz
Windows Binary	GeneGeneInteR_1.16.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	GeneGeneInteR_1.16.0.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