GenomeAnnotatedDataFrame extends AnnotatedDataFrame but requires columns 'isSnp', 'chromosome', and 'position'.
Accessors for the SNP indicator, chromosome, and position are defined for the GenomeAnnotatedDataFrame class
The assayData elements must all be integers. Copy number or relative copy number should be multipled by 100 and stored as an integer. Use integerMatrix(x, 100), where x is a matrix of copy number on the original scale. B allele frequencies should be multipled by 1000 and saved as an integer. Use integerMatrix(b, 1000), where 'b' is a matrix of B allele frequencies.
The featureData in these classes should have the class "GenomeAnnotatedDataFrame".
ocSamples() and ocProbesets() propagate the value they are set to to a cluster (if the cluster is set);
Major refactoring of classes used by SNP/CNP algorithms.
New class: CNSet, AlleleSet, SnpSuperSet
Removed classes: Snp*QSet, Snp*CallSet, Snp*CallSetPlus
Genotyping algorithms will use SnpSet instead of SnpCallSet
Replaced thetaA, thetaB, senseThetaA, antisenseThetaA, senseThetaB and antisenseThetaB methods by allele.
Exported DBPDInfo, ExpressionPDInfo, FeatureSet, TilingPDInfo
Added ff utilities used by both oligo and crlmm packages
bothStrands() methods for AlleleSet and SnpFeatureSet.