1.10版本的变化用户可见的变化使用新闻。CNSet对象中的批处理槽是类'character'(以前，类是'factor')，因此在使用crlmmCopynumber函数分析拷贝数之前，ff包需要进行预处理和基因分型。我们已经在crlmm包中添加了几个关于拷贝数分析的小插图:CopyNumberOverview, AffymetrixPreprocessCN, IlluminaPreprocessCN和Infrastructure。AffymetrixPreprocessCN和IlluminaPreprocessCN小插图分别为Affymetrix和Illumina平台的原始强度的预处理和基因分型提供了说明。“copynumber”和“Infrastructure”小插图适用于Illumina和Affymetrix平台。CopyNumberOverview小插图提供了用于副本数分析的可用小插图的简要摘要。o对于那些对Illumina平台的拷贝数分析感兴趣的人，我们添加了分解预处理和基因分型步骤的函数:constructInf, preprocessInf和genotypeInf。基因型。Illumina函数现在是这些函数的包装器。关于crlmm的额外文档在汇编中提供:http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html 1.8版本的更改USER VISIBLE Changes定义带有batch和batchStatistics槽的CNSet类，不支持CNSetList类，不支持crlmmWrapper, genotype2和crlmmCopynumber2。 Use crlmmCopynumber in place of crlmmWrapper and crlmmCopynumber2. Use genotype instead of genotype2. o raw copy number estimates no longer stored in container. CA and CB methods are no longer simple accessors to data stored in the eset-extension. These functions compute raw copy number estimates from the linear model parameters. Changes in version 1.3 USER VISIBLE CHANGES o 3 new classes created: • 'ABset': container for quantile-normalized A and B intensities for both SNP and copy number probes. Required assay data elements are 'A' and 'B'. Extends eSet directly. 1. For nonpolymorphic probes, the quantile normalized intensity is stored in the 'A' assay data element. The corresponding row in the 'B' assay data element is NA. This is a bit inefficient, but greatly simplifies downstream analyses. In particular, '[' works. • 'CrlmmSetList': container for results from preprocessing and genotyping. This object is a list. The first element of the list is an ABset. The second element is a SnpSet containing genotype calls. The two elements are required to have identical featureNames and sampleNames. 1. added several methods for subsetting and accessing elements of this object, including featureNames, sampleNames, and '['. • 'CopyNumberSet': contains locus-level estimates of copy number for SNPs and polymorphic probes. 1. Required assay data elements are 'CA' and 'CB', corresponding to the absolute copy number for allele A and B, respectively. 2. For nonpolymorphic probes, the total copy number is stored in the 'CA' slot and a NA is recorded for the corresponding row in the CB matrix. 3. Useful methods: 'copyNumber', 'ellipse', 'points' o 'crlmmWrapper' function does preprocessing (quantile-normalization) and genotyping, saving an object of class CrlmmSetList for each chromosome o 'computeCopynumber' now requires an object of class 'CrlmmSetList' and returns an object of class 'CopyNumberSet'.