ParESet-class           Class "ParESet"
ParSnpCallSet-class     Class "ParSnpCallSet"
ParSnpCopyNumberSet-class
                        Class "ParSnpCopyNumberSet"
ParSnpSet-class         Class "ParSnpSet"
addFeatureData-methods
                        Method for Function addFeatureData
alleleA                 Accessor for the A allele
alleleB                 Accessor for the B allele
centromere              Coordinates of centromere
chromosome              Accessors for feature-level SNP annotation
chromosomeAnnotation    chromosome annotation
chromosomeSize          Size of chromosome in number of base pairs.
coerce-methods          Methods for Function coerce
crlmmOut                A data object created by the oligo vignette
cytoband                Start and stop sites of cytoband
dbSnpId                 The dbSNP identifier
enzyme                  Enzyme used to digest DNA
fragmentLength          Accessor for the fragment length
getPar                  Adds graphical parameters for plotting SNP data
hapmap                  Data from the hapmap project
hmmPredict              Accessor for HMM output
integer2chromosome      Converts integer representation of chromosome
                        number back to letter
plotCytoband            Plots idiogram for one chromosome
plotPredictions         Plots the predictions from the HMM
plotSnp                 Plots copy number and genotype calls against
                        physical position
sample.snpset           Example object of class oligoSnpSet
show-methods            show methods
showSummary             Displays descriptive statistics for a sample.
smoothSnp               A simple nonparametric smoother for genotype
                        and copy number
snpPar                  Accessor for graphical parameters
snpset                  Accessor for SNP data
summary-methods         Summary statistics for various SNP classes that
                        extend eSet
updateObject,oligoSnpSet-method
                        updateObject methods
