methylKit 0.99.2

IMPROVEMENTS AND BUG FIXES

• Fixed a bug in methRead() introduced after the addition of mincov argument.
  the bug occurred only reading files legacy text files that have CpGs
  with coverage below 10
• Changes to vignette for better description of the tests.
• Compiler error that occurs in older compilers are fixed via this PR
  #43
• mostly changes to meet BioCcheck() requirements and reccomendations
• C++ code compiles on windows now, regex requirement is no longer there.

methylKit 0.9.6

IMPROVEMENTS AND BUG FIXES

• 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 FUNCTIONS AND FEATURES

• 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
  objects.
• dataSim creates a methylBase object with simulated methylation data.
  A test is added to check this in R CMD check. Contributed by Adrian Bierling.

First release in github