从devel向后移植这个错误修复:将1.19版本news中提到的错误修复恢复到preprocessQuantile。我们的解决方法是错误的;原始代码没有错误。感谢报告该功能问题的用户(弗雷德里克·福尼耶和大卫·马蒂诺)。1.19版更改:o preprocessNoob获取一个dyeMethod参数，现在允许真正的单样本处理。o添加了combineArrayTypes;目的是能够在RGChannelSet级别上结合450k和EPIC阵列数据。o支持EPIC数组中的早期访问IDAT文件。现在使用O message()而不是cat()。o一些函数从弃用变为不使用。 o Addressing a bug in preprocessQuantile which led to reduced performance for Type I probes when run with default paramters (stratified=TRUE). Users are strongly encouraged to update to the latest version (1.19.7 or greater) and rerun the function. o Extended combineArrayTypes to deal with control probes with the same address, but different characteristics (Color, Type, ExtendedType). Discussions with Illumina support reveals that, for control probes, same address is same probe. o Extended combineArrayTypes to support [Genomic](Methyl|Ratio)Set. o Fixed a bug that made detectionP fail with an error if used on only 1 sample. o Fixed a bug in read.metharray where we assumed a certain ordering is consistent in IDAT files from different samples. This is no longer assumed, but as a consequence the function is a bit slower. Bug (indirectly) observed by Giovanni Calice ．o在Biobase 2.33.1中改变MethylSet()的内部结构，以遵循assayDataElement<-的最近变化。o改变MethylSet()的内部(再次)，以遵循Biobase 2.33.2中assayDataElement<-的最近变化。o修复了在pData列没有相同类的各种类上使用combine()的问题。这转化为对combineArrays和estimateCellType的修复。o estimateCellCounts获取一个referencePlatform数组(默认为450k)，现在使用convertArray将输入数据无声地转换到所需的平台。o主要重构注释包，以减少内存消耗。1.15版更改:o增加了preprocessNoob, preprocessFunnorm的测试。o修复preprocessNoob的详细输出。o添加非导出函数. digestvector用于测试。 Changes in version 1.13: o read.450k.exp has support for argument base when targets is supplied. Thanks to Brent Pedersen 注意到这一点并提供了初步解决方案。O改变了read.450k.exp的默认行为。如果使用read.450k创建的targets参数调用。表，您不应该也给它一个基本参数(这总是多余的)。o一些命名空间导入修复。o getGenomicRatioSetFromGEO添加直接从GEO读取并创建一个GenomicsRatioSet。感谢Tim Triche编写原始函数。o makeGenomicRatioSetFromMatrix添加。这个函数将一个矩阵转换为一个GenomicRatioSet。需要提供450K特性id，或者在矩阵的行名中提供。 o makeGenomicRatioSetFromMatrix added to convert matrices to GenomicRatioSets. This can be useful for reading in files with beta values and turning into object that can be directly passed to bumphunter and blockFinder. o readGEORawFile added to read raw intensity files provided as Supplementary Material on GEO. The files include the unmethylated and methylated signals. The new function returns a GenomicMethylSet which permits you to seamlessly apply minfi preprocessing functions. o readTCGA is wrapper for makeGenomicRatioSetFromMatrix that reads in files in the TCGA format. The function is very specific to this format. o Minor coding fixes including some NAMESPACE issues, missing pData<- methods, replace require() with requireNamespace(). o cpgCollapse now works for GenomicRatioSets since it no longer attempts to summarize CN data when passed a GenomicRatioSet. o estimateCellCounts now works on only 2 cell types. o Various NAMESPACE fixes. o the gaphunter function by Shan Andrews has been added. We welcome Shan as a contributing author. Changes in version 1.11: o Updated CITATION. o Added dropLociWithSnps for easy exclusion of certain methylation loci. o Add getAnnotationObject for easy printing of contents of the annotation object. o Changes in 1.10 imported into 1.11. o Fixed an issue with bumphunter calling the bumphunter package in a wrong way. o Added getOOB and getSnpBeta convenience functions for accessing the OOB probes and the SNP probes. o read.450k.sheet now forces a column named Slide to be character. o The NOOB background correction method is now available throguh preprocessNoob. o One can now supply the permutations to be used in permutation analysis. This is useful for cases in which the total number of possilbe permutations is small and one wants to use them all or in cases in which one wants to assure balance, for example, between cases and controls. o The bumphunter method now has the option to create null distributions using a bootstrap approach. o Fixed a man page issue. o Added GitHub URL to DESCRIPTION. o Functional normalization now supports background correction by NOOB (see preprocessNoob); this is recommended (and the new default). Changes in version 1.10: o Modified read.450k.sheet to ignore case when identifying the data header "[DATA]". This addresses an issue with sheets generated by some Illumina instruments. Reported and partial fix provided by the github user nilsigem. Changes in version 1.9: o Importing the changes from 1.8 into 1.9. o Added the withColor argument to the getProbeType function, which allows the return of "IGrn", "IRed", "II", instead of only "I", "II". o Added asList argument to getControlAddress to return result as a list. o Moved reshape from Depends to Imports. o Dramatic improvement in memory usage of preprocessRaw. o Updated CITATION, the minif paper is in press. o Fixed bug with mapToGenome(..., mergeManifest = TRUE) reported by Dale Watkins 还有阿利格拉·a·佩蒂 ．o修复了mapToGenome(rSet)的错误，rSet是一个CN设置为NULL的RatioSet，由allegra a . Petti报告 ．增加了preprocessFunnorm，一个新的预处理方法。o Martin Morgan对获取符号速度的改进 ．如果object是一个GenomicMethylSet，那么version 1.8: o preprocessQuantile(object)中的更改将失败。这是固定的。o清理各种帮助文件中的Rd标记。o estimateCellCounts将抛出错误。这是固定的。函数参数已经改变。o cpgCollapse错误导致错误的结果。如果table(granges(output[[1]])$type)全部为'OpenSea'，则输出将受到影响。Florence Cavalli报道 ．o在'dontrun'中封装了estimateCellCounts()的示例，以便在构建服务器上禁用它。o preprocessQuantile将像removeBadSamples=TRUE一样工作，无论参数的值如何。修复fixMethOutliers中的replace bug;它不会在preprocessSWAN的输出上工作。David mcgauhey报道 ．o函数mapToGenome将返回一些看起来像无序的GenomicMethylSet的东西。实际上，基因座在染色体内的顺序是正确的，问题与染色体的顺序是chr1, chr2, chr3(在minfi中使用)还是chr1, chr10, chr11 (lexigraphically)有关。Florence Cavalli报道 ．o DESCRIPTION中切换到使用新的作者格式。1.7版的更改:o增加了getMethSignal()，一个方便编程的函数。o将getMethSignal()的参数名称“type”更改为“what”。o增加了类“RatioSet”，类似于“GenomicRatioSet”，但没有基因组信息。o修复了“GenomicRatioSet()”构造函数的错误。o增加了方法ratioConvert()，用于将“MethylSet”转换为“RatioSet”或“GenomicMethylSet”转换为“GenomicRatioSet”。修复了基因组甲基set()和基因组ratioset()的问题，这是由于基因组范围包中一个非导出函数的最近变化引起的(由Gustavo Fernandez Bayon报道) )．o在[un]甲基化通道中增加了fixMethOutliers用于阈值极端观测。o增加了getSex, addSex, plotSex用于估计样本的性别。o添加了getQC, addQC, plotQC非常简单的质量控制措施。o增加了minfiQC一站式功能的质量控制措施。改变了一些verbose=TRUE输出在各种函数。o增加了preprocessQuantile。o增加了bumphunter方法“GenomicRatioSet”。o在minfi:::中处理signed 0。在Windows上导致单元测试失败的digestMatrix。 o addSex and addQC lead to sampleNames() being dropped because of a likely bug in cbind(DataFrame, DataFrame). Work-around has been implemented. o Re-ran the test data generator. o Fixed some Depends and Imports issues revealed by new features of R CMD check. o Added blockFinder and cpgCollapse. o (internal) added convenience functions for argument checking. o Exposed and re-wrote getAnnotation(). o Changed getLocations() from being a method to a simple function. Arguments have been removed (for example, now the function always drops non-mapping loci). o Implemented getIslandStatus(), getProbeType(), getSnpInfo() and addSnpInfo(). The two later functions retrieve pre-computed SNP overlaps, and the new annotation object includes SNPs based on dbSNP 137, 135 and 132. o Changed the IlluminaMethylatioAnnotation class to now include genomeBuild information as well as defaults. o Added estimateCellCounts for deconvolution of cell types in whole blood. Thanks to Andrew Jaffe and Andres Houseman. Changes in version 1.5: o Added unit testing for the preprocessing algorithms. o Improved the speed of SWAN for large datasets. o Added the new class "GenomicRatioSet". It is akin to "GenomicMethylSet" but instead of containing Meth and Unmeth it contains M and/or Beta and copy number. o We now depend on illuminaio instead of crlmm in order to get readIDAT. o Added unsrturl.bst to minimize dependences for running Sweave. Changes in version 1.3: o Updated preprocessSwan to fix a bug when mSet was not set to the default value of NULL. Specifically, now the "counts" tables is used to construct "subset". o Changed the function manifestNew() to IlluminaMethylationManifest(). o Added IlluminaMethylationAnnotation(). o Added placeholders for unit testing based on RUnit. o Introduced a new show method for MethylSet and RGChannelSet, derived from the eSet method in Biobase. o The annotation slot of a MethylSet/RGChannelSet is now intended to _not_ be a scalar, but instead have length 2 with components 'array' and 'annotation'. This foreshadows introdution of annotation packages for use with minfi. o Reorganization of R files; rewriting of the man pages for MethylSet, RGChannelSet. o getMeth, getUnmeth, getBeta, getM are now methods. o bug fix to qcReport thanks to Tao Shi. o Changes to getBeta / getM, both in terms of which arguments the methods take and how the values are computed. o Changes to the manifest structure; it now has separate slots for genotype probes and these probes are no longer part of a MethylSet (using eg. preprocessRaw). They can be accessed using getProbeInfo(rgSet, type) with type equal to "SnpI" or "SnpII". o Introduction of mapToGenome, getLocations and the new class GenomicMethylSet. man pages are reasonably complete, still need to add examples to the vignette. This will be a standard part of an extended pipeline. o Introduction of IlluminaHumanMethylation450lannotation.ilmn.v1.2 which contains some new annotation needed for mapToGenome/getLocations. This package will be split into several packages moving forward, in an attempt to harmonize efforts by us and Tim Triche. getLocations/mapToGenome will stay the same. o getControlTypes added (returns the different types of control probes). o GenomicMethylSet now inherits a number of methods including granges(), start(), end() etc. from SummarizedExperiemnt. They have therefore been deleted from minfi. o Bugfix to getLocations(..., mergeManifest = TRUE). It now longer throws an error. o mapToGenome now returns a GenomicMethylSet ordered according to the chromosome name ordering chr1,..,chr22,chrX,chrY,unmapped, the last one not present if drop=TRUE (default). Changes in version 1.1: o Changed NAMESPACE file o Defined constructors for MethylSet, RGChannelSet, RGChannelSetExtended. o Included a version number in the class definition for MethylSet and RGChannelSet. Old objects can be updated by calls of the form updateObject(Mset). o read.manifest (not exported) updated to include nCpGs. o preprocessSwan was added. Still work in progress. o Changed background calculation in preprocessSwan. o Added a section to the vignette describing preprocessSwan. o Bug fix: ilogit2 is now in base (it used to be base e). Thanks to Time Triche, Jr ．o增加并修订了IlluminaMethylationAnnotation类;仍在进行中。o将包小插图从inst/doc移动到小插图。0.99版更改:o Bioconductor的初始版本。o新增新闻文件。o小插图的bug修复。o readaddat现在由crlmm导出，这意味着我们可以通过NAMESPACE导入这个函数。