HmmOptionList           Constructors for HmmOptionList class
HmmOptionList-class     A container for storing options for the hidden
                        Markov model
centerAutosomesAt       Center estimates of copy number for autosomes.
cnEmission              Calculate emission probabilities for total copy
                        number
cnEmission-methods      Methods for Function 'cnEmission' in Package
                        'VanillaICE'
gtEmission              Calculate emission probabilities for genotypes
gtEmission-methods      Methods for calculating the emission
                        probabilities of diallelic genotypes in Package
                        'VanillaICE'
hmm                     Application of the Viterbi algorithm to copy
                        number and/or genotype data.
hmmResults              Example output from hmm
icePlatforms            List platforms for which ICE option is
                        supported.
order,oligoSnpSet-method
                        Methods for oligoSnpSet class
robustSds               Calculate robust estimates of the standard
                        deviation
sd-methods              Methods for estimating copy number standard
                        deviations.
xypanel                 A panel function for plotting copy number
                        versus physical position
xyplot                  Plot copy number and physical position for a
                        set of genomic intervals.
