Changes in version 0.7: o Removed the returnRaw argument to read.bismark() as it was unnecessary (Bismark output files does not have additional information beyond M and Cov and genomic positions, unlike BSmooth). o Moved the Bismark example data from data to inst/extdata. o combineList() now deals with the case where the list of BSseq objects have different genomic locations. This speeds up read.bismark() substantially. o Exposed combineList() as a faster alternative to Reduce(combine, list). o Updated the code for the plotting routines (plotRegion). This should not have an impact on user-visible code. o Added read.bismark() function to parse output from the Bismark alignment suit [thanks to Pete Hickey]. o Refactorized plotting code. Changes in version 0.6: o Fixed a bug in getMeth, where type="raw" resulted in an error for non-smoothed data objects. o Updated CITATION and citations in the vignettes. o Now read.bsmooth supports both gzipped and non-gzipped files, whereas previously it assumed the output files to be gzipped. Thanks to Andreas Schoenegger for reporting this problem. o Fixed a bug in combine() that also resulted in a bug in read.bsmooth when multiple input directories were specified. Bug reported by Andreas Schoenegger. Changes in version 0.4: o Improved combine and fixed a bug. Also added a non-exported combineList for testing. o Bug fix to read.bsmooth; it now works correctly for the default settings (= returning a single object of class BSseq and not a list). o Getting ready for initial release on Bioconductor. o Updated the citations in the vignette(s) and the CITATION file.