AnnotatedSnpSet-class   Deprecated classes
ParESet-class           Class "ParESet"
ParSnpCallSet-class     Class "ParSnpCallSet"
ParSnpCopyNumberSet-class
                        Class "ParSnpCopyNumberSet"
ParSnpSet-class         Class "ParSnpSet"
addFeatureData-methods
                        Method for Function addFeatureData
allPlots                Extracts graphical parameters to be used by all
                        plotting devices
alleleA                 Accessor for the A allele
alleleB                 Accessor for the B allele
calculateCopyNumber-methods
                        Extracts copy number estimates from thetas in
                        SnpQSet object
centromere              Coordinates of centromere
chromosome-methods      Accessor for chromosome SNP annotation
chromosomeAnnotation    chromosome annotation
chromosomeSize          Get size of chromosome in number of base pairs.
coerce-methods          Methods for Function coerce
cytoband                Start and stop sites of cytoband
dbSnpId                 The dbSNP identifier
enzyme                  Enzyme used to digest DNA
fragmentLength          Accessor for the fragment length
getPar-methods          Computes default graphical parameters
getSnpAnnotation        Retrieves SNP-level annotation
hapmap                  Data from the hapmap project
initialize-methods      Generates instances of SnpSet objects
plotCytoband            Plots cytoband for one chromosome
plotSnp                 Plots copy number and genotype calls against
                        physical position
position                Physical position of SNP on chromosome
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
summary-methods         Methods for Function summary
unsplitSnpSet           Combines a list with elements that are
                        AnnotatedSnpSets into one AnnotatedSnpSet.
updateObject,oligoSnpSet-method
                        updateObject methods
