* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 1.0系列新闻* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *第一次包版本。新闻和更新的细节将被添加到这个文件在将来的版本中。1.0.1——pvals函数修改为零用于包括造型的选项。链接在装饰图案arXiv报告补充说。1.0.2,并行版本(通过M3D_Para函数)补充道。生物信息学链接添加到装饰图案。1.0.3——修复警告bioconductor每日构建1.3.3 readENCODEdata——修复bug,基于改变底层rrb BiSeq()函数。这将不会影响工作流。1.3.4更新手册页获得readENCODEdata占之前更新1.3.6优化代码来加快这一进程。现在运行大约快5倍,并行实现显著更好。 1.3.9 Minor speed ups. 1.7.4 Major speedups to main functions. ‘lite’ functions introduced, which are faster and save memory. See the vignette for details. 1.7.5 - 1.7.10 Fixes to pass Bioconductor checks, no changes in workings of package 1.7.11 Added readBedFiles function to read in the different styles of bed file. This replaces readENCODEdata. For the same results, use readBEDFiles with bed_type=‘Encode’ (the default). Details are in the vignette. Also added an error check so that if the files are read in an order that cannot be processed later, an error is called before any work is done. 1.7.12 Added outlier detection to the pvals and pvals_lite functions. This tests for highly variable regions in the null distribution and excludes them from further analysis. Please see the vignette. 1.9.1 Bug fix for readBedFiles. Thanks to Francesca Cairoli of the University of Trieste for the feedback. 1.9.2-3 Removed parallel function due to incompatibility with Windows. I am investigation a cross platform solution in the meantime. Due to speed ups, the sequential ‘lite’ function should be fast enough for all practical needs.