GeneGeneInteR: Tools for Testing Gene-Gene Interaction at the Gene Level
Version 1.2.0

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
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)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneGeneInteR")

Getting started

README.md

Popular man pages

CCA.test: CCA (Canonical-Correlation Analysis) based GGI analysis.
CLD.test: CLD (Composite Linkage Desequilibrium) based GGI analysis.
imputeSnpMatrix: Missing values handling for SnpMatrix object
minP.test: Gene-based Gene-Gene Interaction analysis by combining...
PCA.test: PCA-based Gene-Gene Interaction analysis.
PLSPM.test: PLSPM (Partial Least Squares Path Modelling Analysis) based...
selectSnps: Selects SNPs in snpMatrix and associated info data.frame,...
See all...

All man pages Function index File listing

Man pages

CCA.test: CCA (Canonical-Correlation Analysis) based GGI analysis.
CLD.test: CLD (Composite Linkage Desequilibrium) based GGI analysis.
data.SNP: Multiple genes dataset
gates.test: Gene-based Gene-Gene Interaction analysis by combining...
GBIGM.test: GBIGM (Gene-based information gain method) for GGI analysis.
gene.pair: A case-control dataset with two genes
GGI: Gene-Gene Interaction Analysis of a set of genes
importFile: Imports SNPs information from pedfile, PLINK, VCF (4.0) file,...
imputeSnpMatrix: Missing values handling for SnpMatrix object
KCCA.test: KCCA (Kernel Canonical-Correlation Analysis) based GGI...
minP.test: Gene-based Gene-Gene Interaction analysis by combining...
PCA.test: PCA-based Gene-Gene Interaction analysis.
plot.GGInetwork: Plot a Gene-Gene Interaction Study with an heatmap-like...
PLSPM.test: PLSPM (Partial Least Squares Path Modelling Analysis) based...
print.GGItest: Printing objects of class '"GGItest"'
selectSnps: Selects SNPs in snpMatrix and associated info data.frame,...
snpMatrixScour: SNP filtering based on Minor Allele Frequency, Hardy-Weinberg...
summary.GGInetwork: Printing summaries class '"GGInetwork"' objects
summary.GGItest: Printing summaries class '"GGItest"' objects
tProd.test: Gene-based Gene-Gene Interaction analysis by combining...
tTS.test: Gene-based Gene-Gene Interaction analysis by combining...

Functions

CCA.test Man page Source code
CLD Source code
CLD.test Man page Source code
ChevNy.me Source code
GBIGM.test Man page Source code
GGI Man page Source code
GGI.plot Source code
Galwey.me Source code
GeneScour Source code
InfoGainRat Source code
KCCA.test Man page Source code
Keff.me Source code
LiJi.me Source code
PCA.GenFreq Source code
PCA.Std Source code
PCA.test Man page Source code
PLSPM.test Man page Source code
SSI.BaseTest Source code
SSI.test Source code
base3to10 Source code
clear.tooltip Source code
compare.PCA Source code
data.SNP Man page
draw.colbar Source code
draw.genes.names Source code
draw.interp Source code
draw.matrix Source code
draw.network Source code
draw.tooltip Source code
entropy.vec Source code
estim.var.kz Source code
estim.var.z Source code
gates.test Man page Source code
gene.pair Man page
get.PCA.res Source code
get.U Source code
get.kU Source code
get.kz Source code
get.z Source code
importFile Man page Source code
imputeSnpMatrix Man page Source code
minP.test Man page Source code
minP.test.2pairs Source code
order.snpMatrix Source code
percentofX Source code
plot.GGInetwork Man page Source code
plot.setup Source code
print.GGItest Man page Source code
selectSnps Man page Source code
silence Source code
snpMatrixScour Man page Source code
summary.GGInetwork Man page Source code
summary.GGItest Man page Source code
tProd.stat Source code
tProd.test Man page Source code
tTS.stat Source code
tTS.test Man page Source code

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
GeneGeneInteR documentation built on May 20, 2017, 9:26 p.m.

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