版本1.21.5 o的更改添加了基因集测试功能的功能，以使用户使用基因组限制了感兴趣的基因组区域。o将SIG.GENES参数添加到基因集测试功能中，以允许用户添加重叠每个基因设置为输出的重要基因。o添加了一个修复程序，以避免报告完全零报告的p值。o修改了Varfit函数中COEF的默认值，因此默认值是用于计算Levene残差的设计矩阵的所有列。o更新的小插图包括如何执行如何执行基因集测试后的区域级别分析更改版本1.21.4 o错误修复：修复了导致赔率负值的错误。仅在CPG宇宙小于阵列上的所有CPG，并且一些大型收集的基因比宇宙的基因更小时，才发生错误。版本1.20.3 o的更改添加了fract.Counts逻辑参数以使CPG的分数计数能够在Gometh，Gsameth，Gsameth，Goregion和Gsaregion中关闭。这会关闭映射到多个基因的CPG的调整。这主要用于与早期版本进行比较，我们强烈建议将其设置为真。版本1.20.0 o更新的GSAMETH的更改考虑到某些CPG映射到多个基因。 For a small number of gene families, this previously caused their associated GO categories/gene sets to be erroneously overrepresented and thus highly significant. o Updated gometh to call gsameth to perform statistical testing for GO categories and KEGG pathways; goana and kegga are no longer used. o Replaced use of the AnnotationDbi 'toTable' function with 'select' to speed up execution. o The 'topGSA' function is now used to look at the top ranked results from both gometh and gsameth. The vignette has been modified accordingly. Changes in version 1.15.2 o Updated getMappedEntrezIDs, gometh and gsameth to to speed up execution by taking the array annotation in as an optional argument. o missMethyl now uses the latest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 annotation by default for EPIC arrays. Changes in version 1.15.1 o Added getAdjusted function for extracting RUVm adjusted data for visualisation purposes o Updated vignette to demonstrate use of getAdjusted function o Vignette now includes an example of how to handle cases with RUVm where number of samples is greater than number of Illumina negative controls Changes in version 1.7.3 o modified gene set testing functions gometh and gsameth to accommodate EPIC arrays Changes in version 1.5.1 o New gene set testing function gsameth() added, kegg testing functionality added to gometh. Changes in version 1.1.10 o This version of the package contains functions to perform SWAN normalisation, RUV normalisation and differential methylation analysis, differential variability analysis and gene ontology testing for the 450K array. Changes in version 1.1.3 o Added the gometh function to perform gene ontology analysis. Changes in version 1.1.2 o Added functions to perform RUV normalization and differential methylation analysis. Changes in version 0.99.9 o This version of the package has all calculations in matrix formulation and handles nuisance parameters appropriately. Changes in version 0.99.7 o Added new function, contrasts.varFit. Changes in version 0.99.6 o Modified getLeveneResiduals Changes in version 0.99.5 o Modified the varFit function to accept DGEList objects for differential variability testing for RNA-Seq data. Changes in version 0.99.4 o First version of package contains functions to perform SWAN normalisation and differential variability analysis for DNA methylation data from Illumina's Infinium HumanMethylation450 beadchip.