Recent Releases of methylKit
methylKit - v0.99.2
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 https://github.com/al2na/methylKit/pull/43 - mostly changes to meet BioCcheck() requirements and reccomendations - C++ code compiles on windows now, regex requirement is no longer there.
- R
Published by al2na over 9 years ago
methylKit - more pizza
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.
- R
Published by al2na over 9 years ago