Changes in version 1.18: New class: GenomeAnnotatedDataFrame o GenomeAnnotatedDataFrame extends AnnotatedDataFrame but requires columns 'isSnp', 'chromosome', and 'position'. o Accessors for the SNP indicator, chromosome, and position are defined for the GenomeAnnotatedDataFrame class o 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. o The featureData in these classes should have the class "GenomeAnnotatedDataFrame". Changes in version 1.14: NEW FEATURES o ocSamples() and ocProbesets() propagate the value they are set to to a cluster (if the cluster is set); Changes in version 1.9: USER VISIBLE CHANGES o Major refactoring of classes used by SNP/CNP algorithms. 1. New class: CNSet, AlleleSet, SnpSuperSet 2. Removed classes: Snp*QSet, Snp*CallSet, Snp*CallSetPlus 3. Genotyping algorithms will use SnpSet instead of SnpCallSet o Replaced thetaA, thetaB, senseThetaA, antisenseThetaA, senseThetaB and antisenseThetaB methods by allele. o Exported DBPDInfo, ExpressionPDInfo, FeatureSet, TilingPDInfo o Added ff utilities used by both oligo and crlmm packages NEW FEATURES o bothStrands() methods for AlleleSet and SnpFeatureSet.