ABpanel                 A panel function for plotting prediction
                        regions and log-normalized intensities
CA                      Accessors for allele-specific or total copy
                        number
CA,CNSet-method         crlmm methods for class "CNSet"
Ns                      Accessors for batch-specific summary
                        statistics.
Ns,AssayData-method     Methods for class "AssayData" in crlmm
PredictionRegion-class
                        Class '"PredictionRegion"'
calculateRBaf           Calculate log R ratios and B allele
                        frequencies.
celDates                Extract dates from the cel file header
cnSetExample            Object of class 'CNSet'
constructInf            Instantiate an object of class CNSet for the
                        Infinium platforms.
crlmm                   Genotype oligonucleotide arrays with CRLMM
crlmm-package           Genotype Calling via CRLMM Algorithm
crlmmCopynumber         Locus- and allele-specific estimation of copy
                        number
crlmmIllumina           Genotype Illumina Infinium II BeadChip data
                        with CRLMM
crlmmIlluminaV2         Read and Genotype Illumina Infinium II BeadChip
                        data with CRLMM
genotype                Preprocessing and genotyping of Affymetrix
                        arrays.
genotype.Illumina       Preprocessing and genotyping of Illumina
                        Infinium II arrays.
genotypeInf             Genotyping of Illumina Infinium II arrays.
genotypes               The possible genotypes for an integer copy
                        number.
posteriorProbability    Calculate the posterior probability for integer
                        copy numbers.
predictionRegion        Prediction regions for integer copy number
preprocessInf           Preprocessing of Illumina Infinium II arrays.
readGenCallOutput       Read X and Y intensities from GenCall output
readIDAT                Low-level function to read idat files
readIdatFiles           Reads Idat Files from Infinium II Illumina
                        BeadChips
snprma                  Preprocessing tool for SNP arrays.
xyplot                  Plot prediction regions and normalized
                        intensities.
