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