ABpanel                 A panel function for plotting prediction
                        regions and log-normalized intensities
BafLrrSetList           Methods for Function 'BafLrrSetList' in Package
                        'crlmm' ~~
CA                      Accessors for allele-specific or total copy
                        number
calculateRBaf           Calculate log R ratios and B allele
                        frequencies.
cnrmaAffy               quantile normalize nonpolymorphic markers
cnSetExample            Object of class 'CNSet'
coerce,CNSet,oligoSnpSet-method
                        crlmm methods for class "CNSet"
constructAffyCNSet      Construct an object of class CNSet from
                        Affymetrix cel files
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
genotype                Preprocessing and genotyping of Affymetrix
                        arrays.
genotype.Illumina       Preprocessing and genotyping of Illumina
                        Infinium II arrays.
genotypeAffy            Genotype Affymetrix CEL files
genotypeInf             Genotyping of Illumina Infinium II arrays.
genotypes               The possible genotypes for an integer copy
                        number.
Ns                      Accessors for batch-specific summary
                        statistics.
Ns,AssayData-method     Methods for class "AssayData" in crlmm
plotSNPs                Make M vs S plot for SNPs or samples.
posteriorProbability    Calculate the posterior probability for integer
                        copy numbers.
predictionRegion        Prediction regions for integer copy number
PredictionRegion-class
                        Class '"PredictionRegion"'
preprocessInf           Preprocessing of Illumina Infinium II arrays.
readGenCallOutput       Read X and Y intensities from GenCall output
readIdatFiles           Reads Idat Files from Infinium II Illumina
                        BeadChips
snprma                  Preprocessing tool for SNP arrays.
snprmaAffy              Quantile normalize intensities for SNPs
validCdfNames           Supported annotation packages for crlmm
                        genotyping
validCEL                Reads cel files and return an error if a file
                        is not read
xyplot                  Plot prediction regions and normalized
                        intensities.
