Package: methylInheritance 1.36.0

Astrid Deschênes

methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

Authors:Astrid Deschênes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]

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manual.pdf |manual.html✨
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methylInheritance/json (API)
NEWS

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

Bug tracker:https://github.com/adeschen/methylinheritance/issues

Datasets:
  • demoForTransgenerationalAnalysis - The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
  • methylInheritanceResults - All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
  • samplesForTransgenerationalAnalysis - All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).

On BioConductor:methylInheritance-1.37.0(bioc 3.24)methylInheritance-1.36.0(bioc 3.23)

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencinganalysisbioconductorbioinformaticscpgdifferentially-methylated-elementsinheritancemonte-carlo-samplingpermutation

4.88 score 1 scripts 452 downloads 9 exports 96 dependencies

Last updated from:bbb3471200 (on RELEASE_3_23). Checks:1 WARNING, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING185
linux-devel-x86_64OK576
source / vignettesOK308
linux-release-x86_64OK564
macos-release-arm64OK279
macos-oldrel-arm64OK282
windows-develOK502
windows-releaseOK484
windows-oldrelOK435
wasm-releaseOK175

Exports:calculateSignificantLevelextractInfoloadAllRDSResultsloadConvergenceDatamergePermutationAndObservationplotConvergenceGraphplotGraphrunObservationrunPermutation

Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodacodetoolscpp11crayoncurldata.tableDelayedArrayemdbookfarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmethylKitmgcvmimemvtnormnlmenumDerivopensslplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrebusrebus.baserebus.datetimesrebus.numbersrebus.unicodereshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Inferring inheritance of differentially methylated changes across multiple generations

Astrid Deschênes, Pascal Belleau and Arnaud Droit

Rendered frommethylInheritance.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2018-11-30
Started: 2017-04-07