版本1.29 o v1.29.4的变化修复了检测点中的错误，其中函数始终返回27k数组。由Laurenz Holcik报道。o v1.29.4修复了PreprocessNoob中的错误，其中函数在提供仅具有1个样本的输入数据集时出错（使用默认参数时）。Matt Oldach报道。版本1.27 o v1.27.2的更改修复了在检查先前预处理方法的输入时出现的预处理Quantile（）中的错误。感谢@delnazr的报告（ ）。o v1.27.3使用ConventArray / Combinearrays时，与I型IS的SNP相关的修复错误。Jenny Van Dongen报道。o v1.27.3 DMPFinder中的固定错误。o为Horvathmammalmethylchip40添加了初步支持。版本1.26 o v1.26.1的变化：dmpfinder（）再次工作dat是数字矩阵时。在转换期间，在V1.26.0中引入了此错误以支持DelayedArray支持Minfi对象。感谢@Lowe的报告（＃163）。o将EPIC阵列的默认注释从B2更改为B4。1.25°O的变化增加了DelayedArray备份Minfi对象的初步支持。 This allows disk-backed minfi objects (e.g., using HDF5). This functionality is currently recommended only for developers and advanced users. A user-friendly interface is currently in development. All existing minfi functionality and serialized objects should continue to work as it did in versions prior to 1.25. Please report any problems to the GitHub issue tracker. o Fixing bug in functions readGEORawFile() and getGenomicRatioSetFromGEO(). These two functions did not work (reported an error). They should work now. Thanks to users who reported problems at GitHub issues. o Updated CITATION and citations in the vignette. Changes in version 1.23 o Fixed as() (coercion) from RGChannelSetExtended to RGChannelSet, to support the argument extended=TRUE in read.matharray(). The core issue is the new("RChannelSetExtended") is an invalid object because it does not have correct elements of the assay slot. Instead of addressing this, I used a check for ncol=0, nrow=0 in the coercion function which asssumes the presence of correctly named assays. Original issue report by Stewart Morris 。o改进(使其更美观)read.metharray()和friends中的消息打印。o改变seqlevels(…， force = TRUE)到seqlevel(…,修剪。模式= "粗")。将RGChannelSet、MethylSet和RatioSet从构建在eSet(从Biobase)上移动到summarizedexperexperiment(从summarizedexperexperiment)。最重要的改变是构造函数现在使用参数colData而不是pData;他们中的一些人有更多的争论。updateObject方法已经扩展到更新到新的类后端。虽然pData、sampleNames、featurename方法仍然有效，但我们建议(至少对于包编写者)转移到colData、colnames和rownames。 o Reverted the bugfix to preprocessQuantile mentioned under news for version 1.19. Our fix was wrong; the original code did not have a bug. Thanks to users who reported issues with the function (Frederic Fournier and David Martino). o bugfix for getSnpBeta for subsetted (and combined) RGChannelSets (reported and diagnosed by Warren Cheung). o Accessing the manifest or annotation now fails for an 'unknown' array. o We now support gzipped IDAT files. o Fixed a bug in read.metharray() which resulted in an error in some situations when running the function with argument force=TRUE to read IDAT files of different length. Reported by Maria Calleja Cervantes 。在1.19版本的变化o preprocessNoob获得了dyeMethod参数，现在允许真正的单样例处理。o添加了combineArrayTypes;目的是能够在RGChannelSet级别上组合450k和EPIC数组数据。o支持从EPIC阵列早期访问IDAT文件。现在使用O message()代替cat()。o一些函数从deprecated移到defunct。o解决了preprocessQuantile中的一个bug，当使用默认参数(stratified=TRUE)运行时，它会导致Type I探测的性能下降。强烈建议用户更新到最新版本(1.19.7或更高版本)并重新运行该函数。o扩展组合earraytypes来处理具有相同地址，但不同特征(颜色，类型，ExtendedType)的控制探针。 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更改MethylSet()的内部，以跟上Biobase 2.33.1中assayDataElement<-的最新变化。o更改MethylSet()的内部(再次)，以跟上Biobase 2.33.2中assayDataElement<-的最新变化。修正了不同类上的combine()问题，其中pData列没有相同的类。这转换为对combineArrays和estimateCellType的修复。o estimateCellCounts获得一个referencePlatform数组(默认为450k)，现在使用convertArray静默地将输入数据转换为所需的平台。o主要重构注释包以减少内存消耗。1.15版本的变化o增加了preprocessNoob, preprocessFunnorm的测试。o Fxing preprocessNoob的一些详细输出。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初始修复。o更改了read.450k.exp的默认行为。如果使用Read.450k.sheet创建的目标参数调用，则您不应该给它一个基础参数（始终是多余的）。o一些命名空间导入修复程序。o getGenomicRatiosetfromGeo添加到直接从地理读取并创建GenomicsRATIOSET。感谢Tim Triche写作原始功能。o mapedgenomicratiosetfrommatrix补充道。此功能将矩阵变为GenomicRatioset。需要提供450k的功能ID或矩阵的Rowname。o MakeGenomicRatiosetFrommatrix添加以将矩阵转换为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使用MapTogenome（RSET）的错误是具有RSET的RSET与CN设置为NULL的RASTIOS，由Byallegra A. Petti设置为Null 。o增加了新的预处理方法preprocessFunnorm。o改进的速度getAnnotation马丁摩根 。如果对象是一个GenomicMethylSet，那么1.8版本中preprocessQuantile(object)的更改将失败。这是现在修正。o清理各种帮助文件中的路费降价。o estimateCellCounts将抛出一个错误。这是现在修正。函数参数已经改变。在cpgCollapse错误导致不正确的结果。如果table(granges(output[[1]])$type)全都是'OpenSea'，你的输出会受到影响。Florence Cavalli报道 。o封装在'dontrun'中的rightatecellcounts（）的示例，以在构建服务器上禁用它。o Preprocessquantile会像removeBadsamples一样工作，无论参数的值都是如此。o修复替换夹具中的错误;它不会在Preprocesswan的输出上工作。David McGaughey报道 。o mapToGenome函数将返回一些看起来像无序的genome methylset的东西。实际上，基因座在染色体内的排列是正确的，这个问题与染色体的顺序是chr1, chr2, chr3(在minfi中使用)还是chr1, chr10, chr11(词法上)有关。Florence Cavalli报道 。o在说明中切换到使用新的作者格式。版本1.7 o添加了getMethsignal（）的变化，为编程提供了便利函数。o将“类型”的参数名称更改为getMethsignal（）的“什么”。o添加了“RatioSet”类，如“GenomicRatioset”，但没有基因组信息。o对“genomicratioset（）”构造函数的错误修正。o添加了方法RatioConvert（），用于将“甲基脲”转化为“Ratsetet”或“GenomicRatioset”的“基因组甲基四”。o修复了GenomicMethylset（）和Genomicratioset（）的问题，由最近改变了Genomicranges包中的非出口功能（Gustavo Fernandez Bayon报道 ）。o添加了用于阈值下甲基化通道中的极端观察的修复机器。o添加getsex，addsex，plotsex用于估算样品的性别。o添加GetQc，AddQC，PlotQC，用于非常简单的质量控制措施。o为MINFIQC添加了一个停止功能的质量控制措施。o在各种功能中更改了一些verbose = true输出。o添加了预处理Quantile。o增加了“GenomicRatioset”的Bumphunter方法。o在Minfi :::中处理零归零。DigestMatrix在Windows上导致单元测试失败。由于CBIND（DataFrame，DataFrame）中可能的可能性，odsex和AddQC导致Samplenames（）被丢弃。 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添加并致电了亮amethylationAnnotation类;仍然在progess工作。o从INST / DOC到Vignettes的移动包Vignette。版本0.99 o初始释放到生物导体的变化。o添加了新闻文件。o gugfix到小插图。o ReadIDAT现在由CRLMM导出，意味着我们可以通过命名空间导入此函数。