HmmSnpCallSet-class     Class HmmSnpCallSet
HmmSnpCopyNumberSet-class
                        HmmSnpCopyNumberSet
HmmSnpSet-class         HmmSnpSet
ParHSet-class           Class ParHSet
ParHmmSnpCallSet-class
                        Class ParHmmSnpCallSet
ParHmmSnpCopyNumberSet-class
                        Class ParHmmSnpCopyNumberSet
ParHmmSnpSet-class      Graphical parameters
bind                    Combine two objects of the same class
breakpoints             Locations of breakpoints from the HMM
byArm                   Fits the HMM to each chromosomal arm
calculateEmissionProbability
                        Calculates emission probabilities for the HMM
callEmission            Calculate emission probabilities for the ICE
                        HMM
callsIce                Indicates whether to use confidence estimates
                        of the genotype calls in the HMM
chromosome1             Simulated chromosome 1
chromosomeArm           Accessor for chromosome arm
copyNumberIce           Whether to use the uncertainty estimates of the
                        copy number in the HMM
distance                Accessor for distance
emissionProbability     Accessor for the emission probabilities
getCallEmission         Calculates emission probabilities for genotype
                        calls
getCopyNumberLocation   Typically the mean copy number for the hidden
                        states
getCopyNumberScale      Scale parameter used for Gaussian distribution
                        of copy number
getHapmapProbabilities
                        Estimate probability of correct genotype call
getInitialStateProbability
                        Initial state probabilities
getLohProbability       Emission probabilities for LOH
getTransitionProbability
                        Transition probabilities for the HMM
hSet-class              Virtual class for fitting HMMs to SNP chip data
hapmapProbabilities     CRLMM confidence scores on HapMap data
hmm                     Fits hidden Markov models to high throughput
                        SNP chip data.
hmmBySample             Fits HMM to a single sample
initialStateProbability
                        Retrieves initial state probabilities
isMissing               Checks for missing genotype calls
likelihood              The partial likelihood
locationCopyNumber      Location parameters for the copy number
                        distribution (Gaussian)
numberStates            Number of hidden states
pCHOM                   Probability of a homozygous genotype calls
plotPredictions         Plots the predicted states versus physical
                        position
predictions             Predicted states from the HMM
scaleCopyNumber         Variance parameters for the copy number
                        distribution (Gaussian)
stateNames              The hidden states
transitionProbability   Transition probabilities in the HMM
viterbi                 viterbi algorithm
