@al2na al2na released this Jun 2, 2016 · 572 commits to master since this release

Assets 3

methylKit 0.9.6


  • changes to following function names:
    • read() to methRead()
    • read.bismark to processBismarkAln()
    • adjust.methylC() to adjustMethylC()
    • get.methylDiff() to getMethylDiff()
    • annotate.WithFeature() to annotateWithFeature()
    • annotate.WithFeature.Flank() to annotateWithFeatureFlank()
    • annotate.WithGenicParts() to annotateWithGenicParts()
    • read.bed() to readBed()
    • read.feature.flank() to readFeatureFlank()
    • read.transcript.features() to readTranscriptFeatures()
  • Improved documentation for methRead() (old read())
  • Now, bismark cytosine report and coverage files can be read using methRead()
    pipeline argument. see ?methRead
  • Ported the Perl script for methylation base calling to C/C++ via Rcpp.
    Contributed by Alexander Gosdschan.
  • methRead() uses data.table::fread() to read files faster.


  • new function methSeg() can segment methylation (methylRaw objects) and
    differential methylation (methylDiff objects) profiles to segments.
    Associated function methSeg2bed() creates BED files from segments.
    see ?methSeg. A test is added to check this in R CMD check.
    Contributed by Arsene Wabo and Alexander Gosdschan.
  • new tabix based classes methylRawDB, methylRawListDB, methylBaseDB,
    methylDiffDB and respective methods implemented. Tests are updated to
    check proper function in R CMD check. Contributed by Alexander Gosdschan.
  • calculateDiffMeth() now supports basic overdispersion correction and multiple
    methods for pvalue correction. The function also now handles covariates
    such as age,sex etc. A test is added to check this in R CMD check.
    Contributed by Adrian Bierling.
  • New function calculateDiffMethDSS() is using beta-binomial model from DSS
    package to calculate differential methylation. Contributed by
    Dhruva Chandramohan with modifications from Altuna Akalin. This is a modified
    version of the function from DSS package so that it can work with methylKit
  • dataSim creates a methylBase object with simulated methylation data.
    A test is added to check this in R CMD check. Contributed by Adrian Bierling.