HmmOptions-class        Class "HmmOptions"
HmmOptions-methods      Accessors and replacement methods for
                        HmmOptions
HmmParameter-class      Class "HmmParameter"
HmmPredict-class        Class for the hidden Markov model results
Pi                      Accessor for the initial state probabilities of
                        the hidden Markov model
addFeatureData          Adds chromosomal arm annotation to the
                        featureData
calculateBreakpoints    Calculate breakpoints for altered states from
                        the prediction matrix
calculateCnSE           Calculates copy number standard errors
calculateDistance       Calculates the physical distance between
                        adjacent SNPs
calls.ICE               Indicates whether to use confidence scores of
                        the observed copy number estimates in the HMM
calls.emission          Calculates emission probabilities for the
                        genotype calls
chromosome1             Simulated chromosome 1
copyNumber.ICE          Indicates whether to use confidence scores of
                        the observed copy number estimates in the HMM
copyNumber.emission     Calculate emission probabilities for copy
                        number
copynumberEmission      Emission probabilities for copy number
emission                Accessor for emission probabilities
findBreaks              Identify breakpoints from the hidden Markov
                        model predictions
fit                     Object of class HmmPredict
genomicDistance         A rough estimate of the genomic distance
                        between SNPs
genotypeEmission        Emission probabilities for di-allelic genotype
                        calls
getChromosomeArm        Get the chromosome arm
hmm                     Fits the hidden Markov model
scaleTransitionProbability
                        Scales the probability of transitioning between
                        two states in the Viterbi algorithm
states                  Accessor and replacement method for the hidden
                        states of the Markov model
transitionScale         Scales the transition probabilities of the
                        hidden Markov model
viterbi                 viterbi algorithm
