CNPBayes-package	CNPBayes
bafLikelihood	bafLikelihood
batch	batch-method
batch,MixtureModel-method	batch-method
BatchModel-class	Defunct-classes
BatchModelExample	BatchModelExample
bayesFactor	bayesFactor
bic	bic-method
bic,MultiBatchModel-method	bic-method
burnin	burnin-method
burnin,McmcParams-method	burnin-method
burnin,MixtureModel-method	burnin-method
burnin<-	burnin-method
burnin<-,McmcParams,ANY-method	burnin-method
burnin<-,McmcParams-method	burnin-method
burnin<-,MixtureModel,ANY-method	burnin-method
burnin<-,MixtureModel-method	burnin-method
chains	chains-method
chains,MixtureModel-method	chains-method
chromosome	chromosome
chromosome,GenomicRanges-method	chromosome
CNPBayes	CNPBayes
collapseBatch	collapseBatch-method
collapseBatch,MultiBatchModel-method	collapseBatch-method
collapseBatch,numeric-method	collapseBatch-method
collapseBatch,SummarizedExperiment-method	collapseBatch-method
consensusCNP	consensusCNP
copyNumber	copyNumber
copyNumber,MultiBatchCopyNumber-method	copyNumber
copyNumber,MultiBatchCopyNumberPooled-method	copyNumber
CopyNumberModel	CopyNumber-methods
CopyNumberModel,MultiBatchModel-method	CopyNumber-methods
CopyNumberModel,MultiBatchPooled-method	CopyNumber-methods
CopyNumberModel,SingleBatchModel-method	CopyNumber-methods
DensityBatchModel-class	Defunct-classes
DensityModel-class	Defunct-classes
dfr	dfr-method
dfr,Hyperparameters-method	dfr-method
dfr,MixtureModel,numeric-method	dfr-method
dfr,MixtureModel-method	dfr-method
dfr<-	dfr-method
dfr<-,Hyperparameters,numeric-method	dfr-method
dfr<-,MixtureModel,numeric-method	dfr-method
downSample	downSample
eta.0	eta.0-method
eta.0,Hyperparameters-method	eta.0-method
eta.0,MixtureModel-method	eta.0-method
extract	extract-methods
findSurrogates,MultiBatch-method	findSurrogates-MultiBatch-method
ggChains	ggplot-functions
ggChains,MultiBatchModel-method	ggplot-functions
ggChains,MultiBatchPooled-method	ggplot-functions
ggMixture	ggplot-functions
ggMixture,MultiBatch-method	ggplot-functions
ggMixture,MultiBatchCopyNumber-method	ggplot-functions
ggMixture,MultiBatchCopyNumberPooled-method	ggplot-functions
ggMixture,MultiBatchModel-method	ggplot-functions
ggMixture,MultiBatchPooled-method	ggplot-functions
gibbs	gibbs
hpList	Hyperparameters
Hyperparameters	Hyperparameters
Hyperparameters-class	Hyperparameters-class
HyperparametersBatch-class	HyperparametersBatch-class
HyperparametersMarginal-class	HyperparametersMarginal-class
HyperparametersMultiBatch	HyperparametersMultiBatch
HyperparametersMultiBatch-class	HyperparametersMultiBatch-class
HyperparametersSingleBatch	HyperparametersSingleBatch
HyperparametersSingleBatch-class	HyperparametersSingleBatch-class
HyperparametersTrios	HyperparametersTrios
HyperparametersTrios-class	HyperparametersTrios-class
hyperParams	hyperParams-method
hyperParams,MixtureModel-method	hyperParams-method
hyperParams<-	hyperParams-method
hyperParams<-,MixtureModel,Hyperparameters-method	hyperParams-method
hyperParams<-,MixtureModel-method	hyperParams-method
iter	iter-method
iter,burnin,nStarts,McmcParams-method	McmcParams-class
iter,McmcParams-method	iter-method
iter,MixtureModel-method	iter-method
iter<-	iter-method
iter<-,McmcParams,ANY-method	iter-method
iter<-,McmcParams-method	iter-method
iter<-,MixtureModel,ANY-method	iter-method
iter<-,MixtureModel-method	iter-method
k	k-method
k,Hyperparameters-method	Hyperparameters-class
k,MixtureModel-method	k-method
k,TrioBatchModel-method	k-method
k<-	k-method
k<-,Hyperparameters-method	k-method
k<-,HyperparametersTrios-method	k-method
k<-,MixtureModel-method	k-method
k<-,TrioBatchModel-method	k-method
label_switch	label_switch
label_switch,MixtureModel-method	label_switch
logBayesFactor	logBayesFactor
logPrior	logPrior-method
logPrior,McmcChains-method	logPrior-method
logPrior,MixtureModel-method	logPrior-method
log_lik	log_lik-method
log_lik,McmcChains-method	log_lik-method
log_lik,MixtureModel-method	log_lik-method
m2.0	m2.0-method
m2.0,Hyperparameters-method	m2.0-method
m2.0,MixtureModel-method	m2.0-method
mapCnProbability	mapCnProbability
mapCopyNumber	CopyNumber-methods
mapParams	mapParams
mapping	mapping
mapping,MultiBatchCopyNumber,numeric-method	mapping
mapping,MultiBatchCopyNumber-method	mapping
mapping,MultiBatchCopyNumberPooled,numeric-method	mapping
mapping,MultiBatchCopyNumberPooled-method	mapping
mapping<-	mapping
mapping<-,MultiBatchCopyNumber,character-method	mapping
mapping<-,MultiBatchCopyNumberPooled,character-method	mapping
map_z	map_z
marginalLik	marginalLik
marginalLikelihood	marginalLikelihood-method
marginalLikelihood,list,ANY-method	marginalLikelihood-method
marginalLikelihood,list-method	marginalLikelihood-method
marginalLikelihood,MultiBatchModel,ANY-method	marginalLikelihood-method
marginalLikelihood,MultiBatchModel-method	marginalLikelihood-method
marginalLikelihood,MultiBatchPooled-method	marginalLikelihood-method
MarginalModel-class	Defunct-classes
MarginalModelExample	MarginalModelExample
marginal_lik	marginal_lik
marginal_lik,MixtureModel-method	marginal_lik
marginal_lik<-	marginal_lik
marginal_lik<-,MixtureModel,numeric-method	marginal_lik
MB	MultiBatchModel
MBP	MBP
McmcChains-class	McmcChains-class
McmcParams	McmcParams
mcmcParams	mcmcParams-method
mcmcParams,list-method	mcmcParams-method
mcmcParams,MixtureModel-method	mcmcParams-method
McmcParams-class	McmcParams-class
mcmcParams<-	mcmcParams-method
mcmcParams<-,list,ANY-method	mcmcParams-method
mcmcParams<-,MixtureModel,ANY-method	mcmcParams-method
mcmcParams<-,TrioBatchModel,ANY-method	mcmcParams-method
MixtureModel-class	MixtureModel-class
mlParams	mlParams
modelName,MixtureModel-method	modelName-MixtureModel-method
modes	modes-method
modes,MixtureModel-method	modes-method
modes<-	modes-method
modes<-,MixtureModel-method	modes-method
mu	mu-method
mu,McmcChains-method	mu-method
mu,MixtureModel-method	mu-method
mu,MultiBatchModel-method	mu-method
muc	muc
MultiBatch-class	MultiBatch-class
MultiBatchCopyNumber	CopyNumber-methods
MultiBatchCopyNumber-class	CopyNumber-classes
MultiBatchCopyNumberPooled	CopyNumber-methods
MultiBatchCopyNumberPooled-class	CopyNumber-classes
MultiBatchModel-class	MultiBatchModel-class
MultiBatchModel2	MultiBatchModel
MultiBatchModelExample	MultiBatchModelExample
MultiBatchPooledExample	MultiBatchPooledExample
muMean	muMean
names,McmcChains-method	names-methods
nStarts	nStarts-method
nStarts,McmcParams-method	nStarts-method
nStarts,MixtureModel-method	nStarts-method
nStarts<-	nStarts-method
nStarts<-,McmcParams,ANY-method	nStarts-method
nStarts<-,McmcParams-method	nStarts-method
nStarts<-,MixtureModel,ANY-method	nStarts-method
nStarts<-,MixtureModel-method	nStarts-method
nu.0	nu.0-method
nu.0,McmcChains-method	nu.0-method
nu.0,MixtureModel-method	nu.0-method
numberObs	numberObs-method
numberObs,MixtureModel-method	numberObs-method
oned	oned-method
oned,MixtureModel-method	oned-method
orderModels	orderModels
p,MixtureModel-method	p-MixtureModel-method
pic	pic
posteriorPredictive	posteriorPredictive
posteriorSimulation	posteriorSimulation-method
posteriorSimulation,MixtureModel-method	posteriorSimulation-method
posteriorSimulation,TrioBatchModel-method	posteriorSimulation-method
posterior_cases	posterior_cases
pp	pp
probCopyNumber	probCopyNumber
probCopyNumber,MultiBatchCopyNumber-method	probCopyNumber
probCopyNumber,MultiBatchCopyNumberPooled-method	probCopyNumber
probz	probz-method
probz,MixtureModel-method	probz-method
probzpar	probzpar-method
probzpar,TrioBatchModel-method	probzpar-method
qInverseTau2	qInverseTau2
saveBatch	saveBatch
SB	SingleBatchModel
SBP	SingleBatchModel
sigma	sigma
sigma,MixtureModel-method	sigma2-method
sigma,MultiBatchCopyNumberPooled-method	sigma2-method
sigma2	sigma2-method
sigma2,McmcChains-method	sigma2-method
sigma2,missing-method	sigma2-method
sigma2,MixtureModel-method	sigma2-method
sigma2,MultiBatchCopyNumberPooled-method	sigma2-method
sigma2,MultiBatchPooled-method	sigma2-method
sigma2.0	sigma2.0-method
sigma2.0,McmcChains-method	sigma2.0-method
sigma2.0,MixtureModel-method	sigma2.0-method
sigma2<-,MultiBatchCopyNumberPooled,ANY-method	sigma2-method
sigma2<-,MultiBatchCopyNumberPooled-method	sigma2-method
sigma2<-,MultiBatchPooled,ANY-method	sigma2-method
sigma<-	sigma2-method
sigma<-,MultiBatchCopyNumberPooled-method	sigma2-method
sigmac	sigmac
sigma_,MultiBatchCopyNumberPooled-method	sigma2-method
simulateBatchData	simulateBatchData
simulateData	simulateData
SingleBatchCopyNumber	CopyNumber-methods
SingleBatchCopyNumber-class	CopyNumber-classes
singleBatchGuided,MultiBatchList,MultiBatch-method	singleBatchGuided-MultiBatchList-MultiBatch-method
SingleBatchModel-class	SingleBatchModel-class
SingleBatchModel2	SingleBatchModel
SingleBatchModelExample	SingleBatchModelExample
SingleBatchPooled	SingleBatchModel
tau	tau
tau2	tau2-method
tau2,McmcChains-method	tau2-method
tau2,MixtureModel-method	tau2-method
tauc	tauc
tauMean	tauMean
theta	theta-method
theta,McmcChains-method	theta-method
theta,MixtureModel-method	theta-method
theta<-	theta-method
thin	thin-method
thin,McmcParams-method	thin-method
thin,MixtureModel-method	thin-method
thin<-	thin-method
thin<-,MixtureModel,numeric-method	thin-method
tileMedians	tile-functions
tileSummaries	tile-functions
TrioBatchModel	TrioBatchModel
triodata_lrr	triodata_lrr-method
upSample2	upSample2
y	y-method
y,MixtureModel-method	y-method
z	z-method
z,MixtureModel-method	z-method
zFreq	zfreq-method
zFreq,McmcChains-method	zfreq-method
zfreq,McmcChains-method	zfreq-method
zFreq,MixtureModel-method	zfreq-method
zfreq,MixtureModel-method	zfreq-method
zFreqPar	zfreqpar-method
zFreqPar,McmcChains-method	zfreqpar-method
zfreqpar,McmcChains-method	zfreqpar-method
[,McmcChains,ANY,ANY,ANY-method	extract-methods
[,McmcChains,ANY-method	extract-methods
[,McmcChains-method	extract-methods
[,McmcChainsTrios,ANY,ANY,ANY-method	extract-methods
[,McmcChainsTrios,ANY-method	extract-methods
[,McmcChainsTrios-method	extract-methods
[,MultiBatchModel,ANY,ANY,ANY-method	extract-methods
[,MultiBatchModel,ANY,ANY-method	extract-methods
[,MultiBatchModel,ANY-method	extract-methods
[,MultiBatchModel-method	extract-methods
