1.12.1 DMRcate版本的变化——关闭加速峰值段。R的变化DMRcate版本1.10.2——错误修复没有显著的CpG网站时给定的阈值变化DMRcate版本1.10.1 -数据过滤了史诗数组包含探测信息(通过DMRcatedata_1.8.3)从Pidsley和Zotenko et al。(2016)基因组生物学17 (1),208。——现在可以使用两个新模块在cpg.annotate()除了“微分”和“可变性”:“方差分析”和“diffVar”。“方差分析”会发现试点dmr从整个组对比设计矩阵;“diffVar”发现不同变量地区(DVMRs)使用missMethyl功能包。-类GenomicRatioSet (minfi)现在可以传递给cpg.annotate ()。于改变DMRcate版本1.8.5——dmr现在可以被称为Illumina公司史诗的数组。450 k的工作流是相同的,只是另一种注释参数cpg.annotate()和DMR.plot ()。1.7.2 DMRcate版本——重大变化的变化。WGBS管道现在实现DSS代替limma回归一步。 450K pipeline is the same, but with slight cosmetic changes in anticipation of the transition to the EPIC array. - DMR.plot() has been completely rewritten, now with Gviz and inbuilt transcript annotation for hg19, hg38 and mm10. - DMRs are now ranked by the Stouffer transformations of the limma- and DSS- derived FDRs of their constituent CpG sites. CHANGES IN DMRcate VERSION 1.4.1 - Extra control for Type I error through DMR constituents made commensurate with # of differential limma probes - CITATIONs added CHANGES IN DMRcate VERSION 1.0.2 BUG FIXES • annotate() renamed to cpg.annotate to avoid clashes with same-named function in ggplot2 NEW FEATURES • Kernel estimator has been rewritten from scratch without the need for ks:::kde. Now only takes moderated t-values as cpg weights, as required by the chi-square transformation. • Now allows for multi-level factor experiments, as allowed by limma. Contrasts should be specified with a contrast matrix, otherwise the design matrix MUST have an intercept. (Thanks to Tim Triche Jr. and David Martino for their advice). • A GRanges object can be produced from the results. • XY probes can also be filtered out using rmSNPandCH(). • DMR.plot() allows group median lines to be plotted to better visualise distances between groups (Thanks to Susan van Dijk and Magnus Tobiasson for their advice).