GeneGeneInteR: Tools for Testing Gene-Gene Interaction at the Gene Level

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneGeneInteR")
AuthorMathieu Emily, Nicolas Sounac, Florian Kroell, Magalie Houee-Bigot
Bioconductor views GeneticVariability Genetics GenomeWideAssociation SNP
Date of publicationNone
MaintainerMathieu Emily <mathieu.emily@agrocampus-ouest.fr>, Magalie Houee-Bigot <magalie.houee@agrocampus-ouest.fr>
LicenseGPL (>= 2)
Version1.0.0

View on Bioconductor

Functions

CCA.test Man page
CLD.test Man page
data.SNP Man page
gates.test Man page
GBIGM.test Man page
gene.pair Man page
GGI Man page
importFile Man page
imputeSnpMatrix Man page
KCCA.test Man page
minP.test Man page
PCA.test Man page
plot.GGInetwork Man page
PLSPM.test Man page
print.GGItest Man page
selectSnps Man page
snpMatrixScour Man page
summary.GGInetwork Man page
summary.GGItest Man page
tProd.test Man page
tTS.test Man page

Files

DESCRIPTION
NAMESPACE
R
R/CCA.R R/CLD.R R/GATES.R R/GBIGM.R R/GGI.R R/GGItest.R R/KCCA.R R/PCA.R R/PLSPM.R R/SSIBase.R R/Scour.R R/importFile.R R/imputeSnpMatrix.R R/minP.R R/plot.GGInetwork.R R/print.GGItest.R R/selectSnps.R R/summary.GGInetwork.R R/summary.GGItest.R R/tProd.R R/tTS.R
README.md
build
build/vignette.rds
data
data/data.SNP.rda
data/gene.pair.rda
inst
inst/NEWS
inst/doc
inst/doc/GenePair.R
inst/doc/GenePair.Rnw
inst/doc/GenePair.pdf
inst/doc/VignetteGeneGeneInteR_Introduction.R
inst/doc/VignetteGeneGeneInteR_Introduction.Rnw
inst/doc/VignetteGeneGeneInteR_Introduction.pdf
inst/extdata
inst/extdata/GGIRes.Rdata
inst/extdata/dataImported.Rdata
inst/extdata/dataImputed.Rdata
inst/extdata/dataScour.Rdata
inst/extdata/example.info
inst/extdata/example.ped
inst/extdata/example.txt
inst/extdata/response.txt
man
man/CCA.test.Rd man/CLD.test.Rd man/GBIGM.test.Rd man/GGI.Rd man/KCCA.test.Rd man/PCA.test.Rd man/PLSPM.test.Rd man/data.SNP.Rd man/gates.test.Rd man/gene.pair.Rd man/importFile.Rd man/imputeSnpMatrix.Rd man/minP.test.Rd man/plot.GGInetwork.Rd man/print.GGItest.Rd man/selectSnps.Rd man/snpMatrixScour.Rd man/summary.GGInetwork.Rd man/summary.GGItest.Rd man/tProd.test.Rd man/tTS.test.Rd
vignettes
vignettes/Biblio.bib
vignettes/GGIPlot1.jpg
vignettes/GGIPlot2.jpg
vignettes/GGIPlot3.jpg
vignettes/GGIPlot4.jpg
vignettes/GenePair.Rnw
vignettes/VignetteGeneGeneInteR_Introduction.Rnw
vignettes/network.jpg
vignettes/networkCust.jpg
vignettes/networkD.jpg

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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