变化在1.29版本中o v1.29.4固定一个缺陷在detectionP函数始终返回NA 27 k数组。据Laurenz Holcik。o v1.29.4固定一个缺陷在preprocessNoob函数错误当提供一组输入数据只有1样本(当使用默认参数)。报道了马特Oldach。变化在1.27版本中o v1.27.2修复bug在preprocessQuantile()检查输入时出现之前的预处理方法。感谢@DelnazR报告( )。A和B o v1.27.3固定缺陷相关开关为我当使用convertArray / combineArrays类型的snp。报道了珍妮van幅。o在dmpFinder v1.27.3固定错误。o初步支持HorvathMammalMethylChip40补充道。变化在1.26版本中o v1.26.1: dmpFinder()工作当dat是一个数字矩阵。介绍了这个bug在v1.26.0过渡到支持DelayedArray-backed minfi对象。感谢@ralowe报告(# 163)。o改变默认注释史诗数组从B2 B4。变化在1.25版本中o添加初步支持DelayedArray-backed minfi对象。 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提高(漂亮)的印刷信息read.metharray()和朋友。o改变seqlevels (…力= TRUE) seqlevel (…,修剪。模式= "粗")。变化在1.21版本中o RGChannelSet移动,MethylSet和RatioSet eSet的基础上(从Biobase) SummarizedExperiment(从SummarizedExperiment)。最重要的变化是,现在使用构造函数参数colData pData相反;他们中的一些人有更多的参数。updateObject方法一直延伸到后端更新到新类。虽然pData, sampleNames featureNames方法仍然工作,我们建议(至少对于包作家)colData, colnames 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 。变化在1.19版本中o preprocessNoob得到dyeMethod论点目前允许真正的单一样本处理。o combineArrayTypes添加;目的是能够把450 k和史诗在RGChannelSet数组数据的水平。o支持早期史诗数组访问IDAT文件形式。消息()现在是用来代替阿猫()。求某些函数从已经弃用。o解决一个错误在preprocessQuantile导致降低了I型探测器的性能运行时使用默认的目的(分层= TRUE)。用户强烈建议更新到最新版本(1.19.7或更高)和重新运行功能。o扩展combineArrayTypes处理控制探针具有相同地址,但不同的特征(颜色、类型、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 MethylSet内部的改变()遵循最近的变化在Biobase assayDataElement < - 2.33.1。o MethylSet内部的改变()(再一次)遵循最近的变化在Biobase assayDataElement < - 2.33.2。o修复问题结合()在各种类pData列没有同一个类。这就意味着为combineArrays和estimateCellType修复。o estimateCellCounts得到一系列referencePlatform违约(450 k),现在静静地将输入数据转换成使用convertArray所需的平台。o注释的主要重构方案,以减少内存消耗。变化在1.15版本中添加测试preprocessNoob o, preprocessFunnorm。o fx preprocessNoob的一些详细的输出。o添加non-exported功能.digestVector进行测试。 Changes in version 1.13 o read.450k.exp has support for argument base when targets is supplied. Thanks to Brent Pedersen 注意这和提供了一个初步补丁。o改变read.450k.exp的默认行为。如果使用read.450k创建的目标参数。单,你也不应该给它一个基本论点(这始终是多余的)。o进口修复一些名称空间。o getGenomicRatioSetFromGEO添加到直接从GEO读取并创建一个GenomicsRatioSet。感谢蒂姆Triche写原来的函数。o makeGenomicRatioSetFromMatrix补充道。这个函数把一个矩阵变成GenomicRatioSet。450 k特性id需要提供或rownames的矩阵。 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 和爱兰歌娜Petti 。o mapToGenome固定错误(资源集)与资源集作为RatioSet CN设置为NULL byAllegra a Petti报道 。o preprocessFunnorm补充说,一种新的预处理方法。o改进的速度getAnnotation马丁·摩根 。变化在1.8版本中o preprocessQuantile(对象)将会失败如果对象是一个GenomicMethylSet。这是固定的。o清理Rd减价的各种帮助文件。o estimateCellCounts会抛出一个错误。这是固定的。函数参数发生了变化。o cpgCollapse错误导致不正确的结果。您的输出影响如果表(农庄(输出[[1]])美元类型)都是“OpenSea”。报道了佛罗伦萨卡瓦利 。o封装示例estimateCellCounts ()“dontrun”,构建服务器上禁用它。o preprocessQuantile工作如果removeBadSamples = TRUE不管参数的值。o修复fixMethOutliers取代错误;它不会在preprocessSWAN的输出工作。据大卫McGaughey 。o函数mapToGenome将返回的东西看起来像一个无序GenomicMethylSet。实际上,在染色体位点是正确的命令,这个问题与染色体是否下令chr1, chr2, chr3(用于minfi)或chr1 chr10, chr11 (lexigraphically)。报道了佛罗伦萨卡瓦利 。o转而使用新的作者在描述格式。变化在1.7版本中添加getMethSignal阿(),一个方便的函数编程。o“类型”的参数名称改为“什么”getMethSignal ()。o添加类“RatioSet”,像“GenomicRatioSet”,但没有基因组信息。o修正“GenomicRatioSet()构造函数。o添加方法ratioConvert(),转换为“MethylSet”到“RatioSet”或“GenomicMethylSet”到“GenomicRatioSet”。o GenomicMethylSet固定一个问题()和GenomicRatioSet()由最近的变化导致在GenomicRanges non-exported函数包(Gustavo报道费尔南德斯巴戎寺 )。o添加fixMethOutliers极端观察阈值在[联合国]甲基化渠道。o添加getSex、addSex plotSex估计性的样本。o说getQC addQC, plotQC非常简单的质量控制措施。o说minfiQC一站式功能质量控制措施。o改变了一些详细= TRUE输出各功能。o preprocessQuantile补充道。o添加bumphunter“GenomicRatioSet”的方法。o处理在minfi签署了零:::。在Windows上digestMatrix造成单元测试失败。 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添加和dcoumented IlluminaMethylationAnnotation类;仍然工作在进步。阿包装饰图案从本月/ doc搬到小插曲。变化在0.99版本中o Bioconductor最初版本。添加新闻文件。o错误修复装饰图案。o readIDAT现在由crlmm出口,这意味着我们可以导入这个函数通过名称空间。