addFeatureData	addFeatureData
annotation,HmmOptions-method	HmmOptions-class
annotation<-,HmmOptions,ANY-method	HmmOptions-class
breakpoints	HmmPredict-class
breakpoints,HmmPredict-method	HmmPredict-class
breakpoints<-	HmmPredict-class
breakpoints<-,HmmPredict,ANY-method	HmmPredict-class
breakpoints<-,HmmPredict-method	HmmPredict-class
calculateBreakpoints	calculateBreakpoints
calculateBreakpoints,HmmPredict-method	HmmPredict-class
calculateCnSE	calculateCnSE
calculateDistance	calculateDistance
calculateDistance,HmmOptions-method	HmmOptions-class
calculateDistance,SnpLevelSet-method	calculateDistance
calls.emission	calls.emission
calls.ICE	calls.ICE
calls.ICE,HmmOptions-method	HmmOptions-class
calls.ICE<-	calls.ICE
calls.ICE<-,HmmOptions,logical-method	HmmOptions-class
chromosome,chromosome-method	HmmPredict-class
chromosome,HmmPredict-method	HmmPredict-class
chromosome1	chromosome1
copyNumber.emission	copyNumber.emission
copyNumber.ICE	copyNumber.ICE
copyNumber.ICE,HmmOptions-method	HmmOptions-class
copyNumber.ICE<-	copyNumber.ICE
copyNumber.ICE<-,HmmOptions,logical-method	HmmOptions-class
copyNumber.location	HmmOptions-methods
copyNumber.location,HmmOptions,numeric-method	HmmOptions-class
copyNumber.location,HmmOptions-method	HmmOptions-class
copyNumber.location<-	HmmOptions-methods
copynumberEmission	copynumberEmission
db,HmmOptions-method	HmmOptions-class
emission	emission
emission,HmmParameter-method	HmmParameter-class
emission<-	emission
emission<-,HmmParameter,array-method	HmmParameter-class
fData,HmmPredict-method	HmmPredict-class
featureData,HmmPredict-method	HmmPredict-class
featureNames,HmmPredict-method	HmmPredict-class
findBreaks	findBreaks
fit	fit
genomicDistance	genomicDistance
genomicDistance,HmmParameter-method	HmmParameter-class
genomicDistance<-	genomicDistance
genomicDistance<-,HmmParameter,numeric-method	HmmParameter-class
genotypeEmission	genotypeEmission
getChromosomeArm	getChromosomeArm
getPar,HmmPredict-method	HmmPredict-class
hmm	hmm
hmm,HmmOptions,HmmParameter-method	HmmOptions-class
HmmOptions-class	HmmOptions-class
HmmOptions-methods	HmmOptions-methods
HmmParameter-class	HmmParameter-class
HmmPredict-class	HmmPredict-class
initialize,HmmOptions-method	HmmOptions-class
initialize,HmmParameter-method	HmmParameter-class
initialize,HmmPredict-method	HmmPredict-class
notes,HmmOptions-method	HmmOptions-class
physicalDistance	calculateDistance
physicalDistance,HmmOptions-method	HmmOptions-class
physicalDistance,SnpLevelSet-method	calculateDistance
Pi	pi
Pi,HmmParameter-method	HmmParameter-class
position,HmmPredict-method	HmmPredict-class
predictions	HmmPredict-class
predictions,HmmPredict-method	HmmPredict-class
predictions<-	HmmPredict-class
predictions<-,HmmPredict,matrix-method	HmmPredict-class
probHomCall	HmmOptions-methods
probHomCall,HmmOptions-method	HmmOptions-class
probHomCall<-	HmmOptions-methods
probHomCall<-,HmmOptions,numeric-method	HmmOptions-class
sampleNames,HmmPredict-method	HmmPredict-class
scaleTransitionProbability	scaleTransitionProbability
show,HmmOptions-method	HmmOptions-class
show,HmmParameter-method	HmmParameter-class
show,HmmPredict-method	HmmPredict-class
SnpClass,HmmPredict-method	HmmPredict-class
snpset	HmmOptions-methods
snpset,HmmOptions-method	HmmOptions-class
snpset<-	HmmOptions-methods
snpset<-,HmmOptions,SnpLevelSet-method	HmmOptions-class
states	states
states,HmmOptions-method	HmmOptions-class
states,HmmParameter-method	HmmParameter-class
states,HmmPredict-method	HmmPredict-class
states<-	states
states<-,HmmOptions,character-method	HmmOptions-class
states<-,HmmParameter,character-method	HmmParameter-class
summary,HmmPredict-method	HmmPredict-class
tau	genomicDistance
tau,HmmParameter-method	HmmParameter-class
term5	HmmOptions-methods
term5,HmmOptions-method	HmmOptions-class
term5<-	HmmOptions-methods
term5<-,HmmOptions,numeric-method	HmmOptions-class
transitionScale	transitionScale
transitionScale,HmmParameter-method	HmmParameter-class
transitionScale<-	transitionScale
transitionScale<-,HmmParameter,matrix-method	HmmParameter-class
viterbi	viterbi
[,HmmOptions-method	HmmOptions-class
[,HmmParameter-method	HmmParameter-class
[,HmmPredict-method	HmmPredict-class
