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.

AuthorMathieu Emily, Nicolas Sounac, Florian Kroell, Magalie Houee-Bigot
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

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

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

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All documentation is copyright its authors; we didn't write any of that.