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.

Author
Mathieu Emily, Nicolas Sounac, Florian Kroell, Magalie Houee-Bigot
Date of publication
None
Maintainer
Mathieu Emily <mathieu.emily@agrocampus-ouest.fr>, Magalie Houee-Bigot <magalie.houee@agrocampus-ouest.fr>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

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...

Files in this package

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