Package: epistasisGA 1.9.0

Michael Nodzenski

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:Michael Nodzenski [aut, cre], Juno Krahn [ctb]

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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'))

Peer review:

Bug tracker:https://github.com/mnodzenski/epistasisga/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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-1.9.0(bioc 3.21)epistasisGA-1.8.0(bioc 3.20)

geneticssnpgeneticvariability

4.48 score 1 stars 5 scripts 118 downloads 12 exports 107 dependencies

Last updated 23 days agofrom:a8c940b0eb. Checks:OK: 2 NOTE: 3 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64NOTENov 19 2024
R-4.5-linux-x86_64NOTENov 19 2024
R-4.4-win-x86_64NOTENov 19 2024
R-4.4-mac-x86_64WARNINGNov 19 2024
R-4.4-mac-aarch64WARNINGNov 19 2024
R-4.3-win-x86_64OKNov 19 2024
R-4.3-mac-x86_64WARNINGNov 19 2024
R-4.3-mac-aarch64WARNINGNov 19 2024

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

Michael Nodzenski

Rendered fromIncluding_Maternal_SNPs.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-01-04
Started: 2022-11-11

Detecting GxGxE interactions with case-parent triads using E-GADGETS

Michael Nodzenski

Rendered fromE_GADGETS.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-01-04
Started: 2022-10-26

Use of the GADGETS method to identify multi-SNP effects in nuclear families

Michael Nodzenski

Rendered fromGADGETS.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-12-02
Started: 2022-10-26

Readme and manuals

Help Manual

Help pageTopics
Genotypes for the affected children of case-parent triads.case
Genotypes for the cases of case-parent triads with a simulated gene environment interaction.case.gxe
Genotypes for the affected cases of case-parent triads with a simulated maternal-fetal interaction.case.mci
A function to assign a fitness score to a chromosomechrom.fitness.score
A function to combine GADGETS results for individual islands into a single dataset.combine.islands
A function to compute SNP-pair scores for network plots of results.compute.graphical.scores
Genotypes for the fathers of case-parent triads.dad
Genotypes for the fathers of case-parent triads with a simulated gene environment interaction.dad.gxe
Genotypes for the fathers of case-parent triads with a simulated maternal-fetal interaction.dad.mci
A function to run a test of the null hypothesis that a collection of SNPs do not exhibit epistasis, conditional upon observed marginal SNP-disease associations.epistasis.test
'epistasisGA' packageepistasisGA
Exposures for the cases of case-parent triads with a simulated gene environment interaction.exposure
A function to run the GADGETS methodGADGETS
A function to run a global test of the null hypothesis that there are no SNP-disease associations across a range of chromosome sizesglobal.test
A function to assign an E-GADGETS (GxGxE) fitness score to a chromosomeGxE.fitness.score
A function to run a test of interaction between a collection of SNPs and exposures (experimental).GxE.test
Genotypes for the mothers of case-parent triads.mom
Genotypes for the mothers of case-parent triads with a simulated gene environment interaction.mom.gxe
Genotypes for the mothers of case-parent triads with a simulated maternal-fetal interaction.mom.mci
A function to plot a network of SNPs with potential multi-SNP effects.network.plot
A function to create permuted datasets for permutation based hypothesis testing.permute.dataset
A function to pre-process case-parent triad or disease-discordant sibling data.preprocess.genetic.data
A function to run the GADGETS algorithm to detect multi-SNP effects in case-parent triad studies.run.gadgets
RSID, REF, and ALT annotations for example dataset SNPssnp.annotations
RSID, REF, and ALT annotations for example dataset SNPssnp.annotations.mci