Using NEWS.Rd
batch slot in CNSet objects is class 'character' (previously, class was 'factor')
the ff package is required for preprocessing and genotyping prior to copy number analyses with the crlmmCopynumber function.
We have added several vignettes pertaining to copy number analyses in the crlmm package: CopyNumberOverview, AffymetrixPreprocessCN, IlluminaPreprocessCN, and Infrastructure. The AffymetrixPreprocessCN and IlluminaPreprocessCN vignettes provide instructions for preprocessing and genotyping the raw intensities for Affymetrix and Illumina platforms, respectively. The 'copynumber' and 'Infrastructure' vignettes are applicable to both the Illumina and Affymetrix platforms. The CopyNumberOverview vignette provides a brief summary of the available vignettes for copy number analysis.
For those interested in copy number analysis of Illumina platforms, we added functions that break-down the preprocessing and genotyping steps: constructInf, preprocessInf, and genotypeInf. The genotype.Illumina function is now a wrapper for these functions.
additional documentation for crlmm is provided in a compendium: http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html
define CNSet class with batch and batchStatistics slots
deprecate CNSetList class
deprecate crlmmWrapper, genotype2, and crlmmCopynumber2. Use crlmmCopynumber in place of crlmmWrapper and crlmmCopynumber2. Use genotype instead of genotype2.
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.
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.
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.
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.
Required assay data elements are 'CA' and 'CB', corresponding to the absolute copy number for allele A and B, respectively.
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.
Useful methods: 'copyNumber', 'ellipse', 'points'
'crlmmWrapper' function does preprocessing (quantile-normalization) and genotyping, saving an object of class CrlmmSetList for each chromosome
'computeCopynumber' now requires an object of class 'CrlmmSetList' and returns an object of class 'CopyNumberSet'.