变化在1.17版本中o BSseq()将不再重新排序输入。以前,返回_BSseq_对象被下令位点命令,尽管这种行为没有记录。BSseq()仍可能过滤掉位点如果rmZeroCov = FALSE或崩溃位点strandCollapse = FALSE或重复位点被检测到,但是基因座的相对顺序输出输入的数据匹配。o修复bug BSmooth maxGap争论的()。错误意味着两个甲基化位点的最大差距是不正确地设置为2 *代替maxGap maxGap + 1。这可能并不影响结果的用户离开的默认值maxGap = 10 ^ 8但可能影响结果为小maxGap的价值观。o清理进口和建议。变化在1.13版本中o 1.13.6:修复性能回归BSmooth ()。感谢山安德鲁斯报告( )。o 1.13.5:修复相结合的主要缺陷()和combineList ()。*这错误导致坏BSseq对象不正确的甲基化估计由于不正确的“M”,“浸”,“系数”和“se。系数的化验。*为了安全起见,BSseq创建的对象与版本1.13.0 1.13.4应该重新使用新版本。更具体地说,任何BSseq对象创建组合()或combineList()应该会重现。同时,BSseq创建的对象使用read.bismark()或read.bsmooth()与多个‘文件’应该会重现。由于亚历杭德罗雷耶斯(@areyesq89)报告( )。o 1.13.4:修复性能回归getMeth()和getCoverage()在“地区”提供。由于亚历杭德罗雷耶斯(@areyesq89)报告()。o片段转移到限制型心肌病。变化在1.11版本中o bsseq现在使用DelayedMatrix DelayedArray包的所有矩阵像数据对象。这使得大数据存储在磁盘上,而不是在内存中。o序列化(保存)BSseq、BSseqTstat BSseqStat需要更新对象将通过调用x < - updateObject (x)。变化在1.7版本中o修复一个错误阅读格式中的多个样本与俾斯麦“cytosineReport”。变化在1.5版本中o新函数strandCollapse unstranded正向和反向链数据崩溃。o更新read.bismark()来支持胞嘧啶报告文件;支持两种格式。其他一些小更新(主要是内部)read.bismark ()。 Greatly improved documentation of this function, paying particular attention to differences in file formats between versions of Bismark. 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修正了先前提出的改变(plotRegion)。报道,蒂姆Triche Jr .(修复 。o固定一个严重的错误在朱利安Roux collapseBSseq报道 :使用冰毒值而不是为最终对象的浸浸。然而,这将导致返回对象在所有100%的甲基化位点,所以希望用户将自己见过这个。o固定一个bug combineList使combineList使用“慢”的代码即使在特殊情况更快的快捷方式是可能的。这个bug修复不改变函数的输出在任何输入,只会让它更快。朱利安Roux报道 。现在o有效性检查的存在colnames (sampleNames)被认为是设置,凯文Rue-Albrecht报道 。o固定一个手册页的问题。o稍微改变了引用。o GitHub URL添加到描述。变化在0.9版本中o固定的问题“宽度”的标题bsseq情节。o阴谋。BSseqTstat现在允许BSseqTstat对象没有校正计算。o validObject (BSseq)也已扩展到检查sampleNames一致性。o固定错误相关的有效性检查。o在调用locfit maxk从10000增加到50000,允许拟合模型与unusally长染色体基因组(感谢布莱恩草本报告)。 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.