HmmPredict-class        Class for containing output from a hidden
                        Markov fit to SNP-level data of genotype calls
                        and copy number estimates
ParESet-class           Class "ParESet"
ParSnpCallSet-class     Class "ParSnpCallSet"
ParSnpCopyNumberSet-class
                        Class "ParSnpCopyNumberSet"
ParSnpSet-class         Class "ParSnpSet"
RatioSnpSet-class       Class for high throughput SNP-level data. The
                        assay data contains ratios of copy number.
RatioSnpSet-methods     Accessors for RatioSnpSet objects
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
chromosome2numeric      Converts chromosome to numeric
chromosomeAnnotation    chromosome annotation
chromosomeSize          Get 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
plotCytoband            Plots cytoband 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
selectSomeIndex         Method from Biobase for selecting indices
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         Methods for Function summary
updateObject,oligoSnpSet-method
                        updateObject methods
