Package: GeneGeneInteR 1.33.0

Mathieu Emily

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. <doi:10.18637/jss.v095.i12>.

Authors:Mathieu Emily [aut, cre], Nicolas Sounac [ctb], Florian Kroell [ctb], Magalie Houee-Bigot [aut]

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GeneGeneInteR.pdf |GeneGeneInteR.html✨
GeneGeneInteR/json (API)
NEWS

# Install 'GeneGeneInteR' in R:
install.packages('GeneGeneInteR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:GeneGeneInteR-1.31.0(bioc 3.20)GeneGeneInteR-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genomewideassociationsnpgeneticsgeneticvariability

4.30 score 2 scripts 177 downloads 15 exports 130 dependencies

Last updated 26 days agofrom:bbad5d17b6. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:CCA.testCLD.testgates.testGBIGM.testGGIimportFileimputeSnpMatrixKCCA.testminP.testPCA.testPLSPM.testselectSnpssnpMatrixScourtProd.testtTS.test

Dependencies:abindaskpassbackportsbase64encBHBiocGenericsBiocParallelBiostringsbitopsbootbroombslibcachemcarcarDatacliclustercodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfansifarverfastmapflashClustfontawesomeformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonlitekernlabknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4Vectorssassscalesscatterplot3dsnowsnpStatsSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc

GeneGeneInteR Introduction

Rendered fromVignetteGeneGeneInteR_Introduction.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2016-07-19
Started: 2016-07-19

Pairwise interaction tests

Rendered fromGenePair.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2016-12-03
Started: 2016-07-19

Readme and manuals

Help Manual

Help pageTopics
CCA (Canonical-Correlation Analysis) based GGI analysis.CCA.test
CLD (Composite Linkage Desequilibrium) based GGI analysis.CLD.test
Multiple genes datasetdata.SNP
Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction testsgates.test
GBIGM (Gene-based information gain method) for GGI analysis.GBIGM.test
A case-control dataset with two genesgene.pair
Gene-Gene Interaction Analysis of a set of genesGGI
Imports SNPs information from pedfile, PLINK, VCF (4.0) file, or genotypes imputed by IMPUTE2.importFile
Missing values handling for SnpMatrix objectimputeSnpMatrix
KCCA (Kernel Canonical-Correlation Analysis) based GGI analysis.KCCA.test
Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction testsminP.test
PCA-based Gene-Gene Interaction analysis.PCA.test
Plot a Gene-Gene Interaction Study with an heatmap-like visualizationplot.GGInetwork
PLSPM (Partial Least Squares Path Modelling Analysis) based Gene-Gene Interaction analysis.PLSPM.test
Printing objects of class '"GGItest"'print.GGItest
Selects SNPs in snpMatrix and associated info data.frame, outputs of importFile.selectSnps
SNP filtering based on Minor Allele Frequency, Hardy-Weinberg Equilibrium and call ratesnpMatrixScour
Printing summaries class '"GGInetwork"' objectssummary.GGInetwork
Printing summaries class '"GGItest"' objectssummary.GGItest
Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction teststProd.test
Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction teststTS.test