1.10版本的变化:用户可见的变化使用消息啊。Rd o批槽在CNSet对象是类“字符”(以前,类是“因素”)o ff包需要预处理和基因拷贝数分析之前crlmmCopynumber函数。o我们已经添加了几个小插曲与拷贝数分析crlmm包:CopyNumberOverview, AffymetrixPreprocessCN IlluminaPreprocessCN和基础设施。AffymetrixPreprocessCN IlluminaPreprocessCN小品文提供指令预处理和基因分型的原始强度Affymetrix和Illumina公司平台,分别。“copynumber”和“基础设施”的小插曲适用于Illumina公司和Affymetrix平台。CopyNumberOverview故事提供了一个简短的总结为拷贝数分析可用的小插曲。o为那些感兴趣的拷贝数分析Illumina公司平台,我们添加了功能分解预处理和步骤:pcr constructInf, preprocessInf, genotypeInf。基因型。Illumina公司现在是一个包装器函数,这些函数。o额外的文档提供了crlmm纲要:http://www.biostat.jhsph.edu/ rscharpf / crlmmCompendium / index . html 1.8版本的变化:用户可见的变化与批处理和batchStatistics槽o o定义CNSet类反对CNSetList类o轻视crlmmWrapper, genotype2, 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'.