Changes in version 0.11: o Converted to using Authors@R in the DESCRIPTIOn file. o plotRegion did not respect the col/lty/lwd argument if given explicitely as opposed to through pData(). Reported by Karen Conneely . o Fixed an issue introduced by the previous change (to plotRegion). Reported (with a fix) by Tim Triche Jr . o Fixed a serious bug in collapseBSseq reported by Julien Roux : it would use the Meth values instead of Cov for the final object's Cov. However, this will result in the return object having a methylation of 100 percent across all loci, so hopefully users will have seen this for themselves. o Fixed a bug in combineList which made combineList use "slow" code even in a special case where a faster shortcut was possible. This bug fix does not change the output of the function under any input, it only makes it faster. Reported by Julien Roux . o validity now checks for the presence of colnames (sampleNames) which was assumed to be set. Reported by Kevin Rue-Albrecht . o Fixed a man page issue. o Slightly changed CITATION. o Added GitHub URL to DESCRIPTION. Changes in version 0.9: o Fixed a problem with "width" in the title of bsseq plots. o plot.BSseqTstat now allows for BSseqTstat objects computed without correction. o validObject(BSseq) has been extended to also check for sampleNames consistency. o Fixed a bug related to validity checking. o Increased maxk from 10,000 to 50,000 in calls to locfit, to allowing fitting the model on genomes with unusally long chromosomes (Thanks to Brian Herb for reporting). o The class representation for class 'BSseq' has changed completely. The new class is build on 'SummarizedExperiment' from GenomicRanges instead of 'hasGRanges'. Use 'x <- updateObject(x)' to update serialized (saved) objects. o Fixing a problem in orderBSseq related to chromosome names. o Allowed user specification of maxk, with a default of 10,000 in BSmooth. o Many bugfixes made necessary by the new class representation. o Better argument checking in BSmooth.tstat. o A few undocumented functions are now documented. o Rewrote orderBSseq 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.