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* 1.3 SERIES NEWS *
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USER VISIBLE CHANGES
o 3 new classes created:
i. '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.
ii. '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 "[".
iii. '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'
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'.
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