.unsplitHmm	HmmSnpSet-class
.unsplitHmm,list,AnnotatedDataFrame-method	HmmSnpSet-class
bind	bind
bind,HmmSnpCallSet,HmmSnpCallSet-method	HmmSnpCallSet-class
bind,HmmSnpCallSet,NULL-method	HmmSnpCallSet-class
bind,HmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
bind,HmmSnpCopyNumberSet,NULL-method	HmmSnpCopyNumberSet-class
bind,HmmSnpSet,HmmSnpSet-method	HmmSnpSet-class
bind,HmmSnpSet,NULL-method	HmmSnpSet-class
bind,NULL,HmmSnpCallSet-method	HmmSnpCallSet-class
bind,NULL,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
bind,NULL,HmmSnpSet-method	HmmSnpSet-class
breakpoints	breakpoints
breakpoints,HmmSnpSet-method	HmmSnpSet-class
breakpoints,hSet-method	hSet-class
byArm	byArm
byArm,hSet-method	hSet-class
calculateEmissionProbability	calculateEmissionProbability
calculateEmissionProbability,HmmSnpCallSet-method	HmmSnpCallSet-class
calculateEmissionProbability,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
calculateEmissionProbability,HmmSnpSet-method	HmmSnpSet-class
callEmission	callEmission
callsIce	callsIce
callsIce,HmmSnpCallSet-method	HmmSnpCallSet-class
callsIce,hSet-method	hSet-class
callsIce<-	callsIce
callsIce<-,HmmSnpCallSet,logical-method	HmmSnpCallSet-class
callsIce<-,hSet,logical-method	hSet-class
chromosome1	chromosome1
chromosomeArm	chromosomeArm
chromosomeArm,hSet-method	hSet-class
chromosomeArm<-	chromosomeArm
chromosomeArm<-,hSet-method	hSet-class
coerce,HmmSnpSet,HmmSnpCallSet-method	HmmSnpCallSet-class
coerce,HmmSnpSet,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
coerce,oligoSnpSet,HmmSnpCallSet-method	HmmSnpCallSet-class
coerce,oligoSnpSet,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
coerce,oligoSnpSet,HmmSnpSet-method	HmmSnpSet-class
coerce,SnpCallSet,HmmSnpCallSet-method	HmmSnpCallSet-class
coerce,SnpCopyNumberSet,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
copyNumberIce	copyNumberIce
copyNumberIce,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
copyNumberIce,hSet-method	hSet-class
copyNumberIce<-	copyNumberIce
copyNumberIce<-,HmmSnpCopyNumberSet,logical-method	HmmSnpCopyNumberSet-class
copyNumberIce<-,hSet,logical-method	hSet-class
distance	distance
distance,hSet-method	hSet-class
distance<-	distance
distance<-,hSet-method	hSet-class
emissionProbability	emissionProbability
emissionProbability,hSet-method	hSet-class
emissionProbability<-	emissionProbability
emissionProbability<-,hSet-method	hSet-class
getBreaks	hSet-class
getBreaks,hSet-method	hSet-class
getCallEmission	getCallEmission
getCopyNumberLocation	getCopyNumberLocation
getCopyNumberLocation,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
getCopyNumberLocation,HmmSnpSet-method	HmmSnpSet-class
getCopyNumberScale	getCopyNumberScale
getCopyNumberScale,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
getCopyNumberScale,HmmSnpSet-method	HmmSnpSet-class
getHapmapProbabilities	getHapmapProbabilities
getInitialStateProbability	getInitialStateProbability
getInitialStateProbability,HmmSnpCallSet-method	HmmSnpCallSet-class
getInitialStateProbability,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
getInitialStateProbability,HmmSnpSet-method	HmmSnpSet-class
getLohProbability	getLohProbability
getLohProbability,HmmSnpCallSet-method	HmmSnpCallSet-class
getLohProbability,HmmSnpSet-method	HmmSnpSet-class
getPar,hSet-method	hSet-class
getTransitionProbability	getTransitionProbability
getTransitionProbability,HmmSnpCallSet-method	HmmSnpCallSet-class
getTransitionProbability,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
getTransitionProbability,HmmSnpSet-method	HmmSnpSet-class
hapmapProbabilities	hapmapProbabilities
hmm	hmm
hmm,HmmSnpCallSet-method	HmmSnpCallSet-class
hmm,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
hmm,HmmSnpSet-method	HmmSnpSet-class
hmmBySample	hmmBySample
hmmBySample,hSet-method	hSet-class
HmmSnpCallSet-class	HmmSnpCallSet-class
HmmSnpCopyNumberSet-class	HmmSnpCopyNumberSet-class
HmmSnpSet-class	HmmSnpSet-class
hSet-class	hSet-class
ice2VanillaICE	HmmSnpSet-class
ice2VanillaICE,HmmSnpSet-method	HmmSnpSet-class
initialize,HmmSnpCallSet-method	HmmSnpCallSet-class
initialize,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
initialize,HmmSnpSet-method	HmmSnpSet-class
initialize,ParHmmSnpCallSet-method	ParHmmSnpCallSet-class
initialize,ParHmmSnpCopyNumberSet-method	ParHmmSnpCopyNumberSet-class
initialize,ParHmmSnpSet-method	ParHmmSnpSet-class
initialize,ParHSet-method	ParHSet-class
initialStateProbability	initialStateProbability
initialStateProbability,hSet-method	hSet-class
initialStateProbability<-	initialStateProbability
initialStateProbability<-,hSet-method	hSet-class
isMissing	isMissing
isMissing,HmmSnpCallSet-method	HmmSnpCallSet-class
isMissing,hSet-method	hSet-class
likelihood	likelihood
likelihood,hSet-method	hSet-class
likelihood<-	likelihood
likelihood<-,hSet-method	hSet-class
locationCopyNumber	locationCopyNumber
locationCopyNumber,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
locationCopyNumber,HmmSnpSet-method	HmmSnpSet-class
locationCopyNumber<-	locationCopyNumber
locationCopyNumber<-,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
locationCopyNumber<-,HmmSnpSet-method	HmmSnpSet-class
numberStates	numberStates
numberStates,hSet-method	hSet-class
numberStates<-	numberStates
ParHmmSnpCallSet-class	ParHmmSnpCallSet-class
ParHmmSnpCopyNumberSet-class	ParHmmSnpCopyNumberSet-class
ParHmmSnpSet-class	ParHmmSnpSet-class
ParHSet-class	ParHSet-class
pCHOM	pCHOM
pCHOM,HmmSnpCallSet-method	HmmSnpCallSet-class
pCHOM,HmmSnpSet-method	HmmSnpSet-class
pCHOM<-	pCHOM
pCHOM<-,HmmSnpCallSet-method	HmmSnpCallSet-class
pCHOM<-,HmmSnpSet-method	HmmSnpSet-class
plotPredictions	plotPredictions
plotSnp,hSet-method	hSet-class
plotSnp,ParHmmSnpCallSet,HmmSnpCallSet-method	ParHmmSnpCallSet-class
plotSnp,ParHmmSnpCopyNumberSet,HmmSnpCopyNumberSet-method	ParHmmSnpCopyNumberSet-class
plotSnp,ParHmmSnpSet,HmmSnpSet-method	ParHmmSnpSet-class
plotSnp,ParHSet,ANY-method	ParHSet-class
predictions	predictions
predictions,HmmSnpSet-method	HmmSnpSet-class
predictions,hSet-method	hSet-class
predictions<-	predictions
predictions<-,HmmSnpSet,matrix-method	HmmSnpSet-class
predictions<-,hSet,ANY-method	hSet-class
scaleCopyNumber	scaleCopyNumber
scaleCopyNumber,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
scaleCopyNumber,HmmSnpSet-method	HmmSnpSet-class
scaleCopyNumber<-	scaleCopyNumber
scaleCopyNumber<-,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
scaleCopyNumber<-,HmmSnpSet-method	HmmSnpSet-class
show,HmmSnpCallSet-method	HmmSnpCallSet-class
show,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
show,HmmSnpSet-method	HmmSnpSet-class
stateNames	stateNames
stateNames,hSet-method	hSet-class
stateNames<-	stateNames
stateNames<-,hSet-method	hSet-class
transitionProbability	transitionProbability
transitionProbability,hSet-method	hSet-class
transitionProbability<-	transitionProbability
transitionProbability<-,hSet-method	hSet-class
viterbi	viterbi
viterbi,hSet-method	hSet-class
[,HmmSnpCallSet-method	HmmSnpCallSet-class
[,HmmSnpCopyNumberSet-method	HmmSnpCopyNumberSet-class
[,HmmSnpSet-method	HmmSnpSet-class
[<-,HmmSnpSet-method	HmmSnpSet-class
