Package: epistasisGA 1.7.0
epistasisGA: An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.
Authors:
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epistasisGA.pdf |epistasisGA.html✨
epistasisGA/json (API)
# Install 'epistasisGA' in R: |
install.packages('epistasisGA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mnodzenski/epistasisga/issues
- case - Genotypes for the affected children of case-parent triads.
- case.gxe - Genotypes for the cases of case-parent triads with a simulated gene environment interaction.
- case.mci - Genotypes for the affected cases of case-parent triads with a simulated maternal-fetal interaction.
- dad - Genotypes for the fathers of case-parent triads.
- dad.gxe - Genotypes for the fathers of case-parent triads with a simulated gene environment interaction.
- dad.mci - Genotypes for the fathers of case-parent triads with a simulated maternal-fetal interaction.
- exposure - Exposures for the cases of case-parent triads with a simulated gene environment interaction.
- mom - Genotypes for the mothers of case-parent triads.
- mom.gxe - Genotypes for the mothers of case-parent triads with a simulated gene environment interaction.
- mom.mci - Genotypes for the mothers of case-parent triads with a simulated maternal-fetal interaction.
- snp.annotations - RSID, REF, and ALT annotations for example dataset SNPs
- snp.annotations.mci - RSID, REF, and ALT annotations for example dataset SNPs
On BioConductor:epistasisGA-1.7.0(bioc 3.20)epistasisGA-1.6.0(bioc 3.19)
Last updated 2 months agofrom:2374862e43
Exports:chrom.fitness.scorecombine.islandscompute.graphical.scoresepistasis.testGADGETSglobal.testGxE.fitness.scoreGxE.testnetwork.plotpermute.datasetpreprocess.genetic.datarun.gadgets
Dependencies:abindbackportsbase64encbase64urlbatchtoolsBHbigmemorybigmemory.sriBiocParallelbrewbslibcachemcheckmatecliclustercodetoolscolorspacecorpcorcpp11crayondata.tabledigestevaluatefansifarverfastmapfdrtoolfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsggplot2glassoglueGPArotationgridExtragtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetsigraphisobandjpegjquerylibjsonliteknitrlabelinglambda.rlatticelavaanlifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemnormtmunsellnlmennetnumDerivpbapplypbivnormpillarpkgconfigplyrpngprettyunitsprogresspsychqgraphquadprogR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownrpartrstudioapisassscalessnowstringistringrsurvivaltibbletinytexutf8uuidvctrsviridisviridisLitewithrxfunyaml
Using the GADGETS method to detect epistatic maternally-mediated effects and maternal-fetal interactions
Rendered fromIncluding_Maternal_SNPs.Rmd
usingknitr::rmarkdown
on Jul 06 2024.Last update: 2023-01-04
Started: 2022-11-11
Detecting GxGxE interactions with case-parent triads using E-GADGETS
Rendered fromE_GADGETS.Rmd
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on Jul 06 2024.Last update: 2023-01-04
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Use of the GADGETS method to identify multi-SNP effects in nuclear families
Rendered fromGADGETS.Rmd
usingknitr::rmarkdown
on Jul 06 2024.Last update: 2022-12-02
Started: 2022-10-26