CNPBayes-package	CNPBayes
batch	batch-method
batch,DensityModel-method	Deprecated-functions
batch,MixtureModel-method	batch-method
BatchModel	Deprecated-functions
BatchModel-class	Deprecated-classes
BatchModelExample	BatchModelExample
BatchModelList	Deprecated-functions
bic	bic-method
bic,BatchModel-method	bic-method
bic,MarginalModel-method	Deprecated-functions
bic,MultiBatchModel-method	bic-method
bic,SingleBatchModel-method	bic-method
burnin	burnin-method
burnin,McmcParams-method	burnin-method
burnin,MixtureModel-method	burnin-method
burnin<-	burnin-method
burnin<-,McmcParams-method	burnin-method
burnin<-,MixtureModel-method	burnin-method
chains	chains-method
chains,MixtureModel-method	chains-method
chromosome	chromosome
clusters	Deprecated-functions
CNPBayes	CNPBayes
collapseBatch	collapseBatch-method
collapseBatch,BatchModel-method	collapseBatch-method
collapseBatch,MultiBatchModel-method	collapseBatch-method
collapseBatch,numeric-method	collapseBatch-method
collapseBatch,SummarizedExperiment-method	collapseBatch-method
combinePlates	combinePlates-method
combinePlates,numeric-method	combinePlates-method
consensusCNP	consensusCNP
copyNumber	copyNumber
copyNumber,MultiBatchCopyNumber-method	copyNumber
copyNumber,SingleBatchCopyNumber-method	copyNumber
CopyNumberModel	CopyNumber-methods
CopyNumberModel,MultiBatchModel-method	CopyNumber-methods
CopyNumberModel,MultiBatchPooled-method	CopyNumber-methods
CopyNumberModel,SingleBatchModel-method	CopyNumber-methods
DensityBatchModel-class	Deprecated-classes
DensityModel	Deprecated-functions
DensityModel-class	Deprecated-classes
downsample	Deprecated-functions
downSampleEachBatch	Deprecated-functions
eta.0	eta.0-method
eta.0,Hyperparameters-method	eta.0-method
eta.0,MixtureModel-method	eta.0-method
extract	extract-methods
ggChains	ggplot-functions
ggChains,MultiBatchModel-method	ggplot-functions
ggChains,MultiBatchPooled-method	ggplot-functions
ggChains,SingleBatchModel-method	ggplot-functions
ggChains,SingleBatchPooled-method	ggplot-functions
ggMixture	ggplot-functions
ggMixture,MultiBatchCopyNumber-method	ggplot-functions
ggMixture,MultiBatchCopyNumberPooled-method	ggplot-functions
ggMixture,MultiBatchModel-method	ggplot-functions
ggMixture,MultiBatchPooled-method	ggplot-functions
ggMixture,SingleBatchCopyNumber-method	ggplot-functions
ggMixture,SingleBatchModel-method	ggplot-functions
ggMultiBatch	ggplot-functions
ggMultiBatch,BatchModel-method	Deprecated-functions
ggMultiBatch,MultiBatchCopyNumber-method	Deprecated-functions
ggMultiBatch,MultiBatchModel-method	Deprecated-functions
ggMultiBatch,MultiBatchPooled-method	Deprecated-functions
ggPredictive	ggPredictive
ggSingleBatch	ggplot-functions
ggSingleBatch,MarginalModel-method	Deprecated-functions
ggSingleBatch,SingleBatchCopyNumber-method	Deprecated-functions
ggSingleBatch,SingleBatchModel-method	Deprecated-functions
ggSingleBatchChains	ggplot-functions
gibbs	gibbs
gibbs_all	gibbs_all
gibbs_pooled	gibbs_pooled
hpList	Hyperparameters
Hyperparameters	Hyperparameters
Hyperparameters-class	Hyperparameters-class
HyperparametersBatch	Deprecated-functions
HyperparametersBatch-class	HyperparametersBatch-class
HyperparametersMarginal	Deprecated-functions
HyperparametersMarginal-class	HyperparametersMarginal-class
HyperparametersMultiBatch	HyperparametersMultiBatch
HyperparametersMultiBatch-class	HyperparametersMultiBatch-class
HyperparametersSingleBatch	HyperparametersSingleBatch
HyperparametersSingleBatch-class	HyperparametersSingleBatch-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-method	iter-method
iter<-,MixtureModel-method	iter-method
k	k-method
k,DensityModel-method	Deprecated-functions
k,Hyperparameters-method	Hyperparameters-class
k,MixtureModel-method	k-method
k<-	k-method
k<-,Hyperparameters-method	k-method
k<-,Hyperparemeters-method	k-method
k<-,MixtureModel-method	k-method
labelSwitching	Deprecated-functions
labelSwitching,MixtureModel-method	Deprecated-functions
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
mapComponents	mapComponents
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,SingleBatchCopyNumber,numeric-method	mapping
mapping,SingleBatchCopyNumber-method	mapping
mapping<-	mapping
mapping<-,MultiBatchCopyNumber,numeric-method	mapping
mapping<-,MultiBatchCopyNumberPooled,numeric-method	mapping
mapping<-,SingleBatchCopyNumber,numeric-method	mapping
map_z	map_z
marginalLikelihood	marginalLikelihood-method
marginalLikelihood,BatchModel,ANY-method	Deprecated-functions
marginalLikelihood,BatchModel-method	Deprecated-functions
marginalLikelihood,list,ANY-method	marginalLikelihood-method
marginalLikelihood,list-method	marginalLikelihood-method
marginalLikelihood,MarginalModel,ANY-method	Deprecated-functions
marginalLikelihood,MarginalModel-method	Deprecated-functions
marginalLikelihood,MultiBatchModel,ANY-method	marginalLikelihood-method
marginalLikelihood,MultiBatchModel-method	marginalLikelihood-method
marginalLikelihood,MultiBatchPooled-method	marginalLikelihood-method
marginalLikelihood,SingleBatchModel,ANY-method	marginalLikelihood-method
marginalLikelihood,SingleBatchModel-method	marginalLikelihood-method
marginalLikelihood,SingleBatchPooled,ANY-method	marginalLikelihood-method
marginalLikelihood,SingleBatchPooled-method	marginalLikelihood-method
MarginalModel-class	Deprecated-classes
MarginalModelExample	MarginalModelExample
marginal_lik	marginal_lik
marginal_lik,MixtureModel-method	marginal_lik
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-method	mcmcParams-method
mcmcParams<-,MixtureModel-method	mcmcParams-method
MixtureModel-class	MixtureModel-class
mlParams	mlParams
modes	modes-method
modes,DensityModel-method	Deprecated-functions
modes,MixtureModel-method	modes-method
modes<-	modes-method
modes<-,MixtureModel-method	modes-method
mu	mu-method
mu,BatchModel-method	mu-method
mu,MarginalModel-method	mu-method
mu,McmcChains-method	mu-method
mu,MultiBatchModel-method	mu-method
mu,SingleBatchModel-method	mu-method
muc	muc
MultiBatchCopyNumber	CopyNumber-methods
MultiBatchCopyNumberPooled	CopyNumber-methods
multiBatchDensities	Deprecated-functions
MultiBatchModel	Deprecated-functions
MultiBatchModel-class	MultiBatchModel-class
MultiBatchModel2	MultiBatchModel2
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-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
p	p
pic	pic
plot	Deprecated-functions
plot,BatchModel,ANY-method	Deprecated-functions
plot,DensityBatchModel,ANY-method	Deprecated-functions
plot,DensityModel,ANY-method	Deprecated-functions
plot,DensityModel,numeric-method	Deprecated-functions
plot,MarginalModel,ANY-method	Deprecated-functions
posteriorPredictive	posteriorPredictive
posteriorSimulation	posteriorSimulation-method
posteriorSimulation,list,ANY-method	Deprecated-functions
posteriorSimulation,list-method	Deprecated-functions
posteriorSimulation,MixtureModel,ANY-method	posteriorSimulation-method
posteriorSimulation,MixtureModel,integer-method	Deprecated-functions
posteriorSimulation,MixtureModel,numeric-method	Deprecated-functions
posteriorSimulation,MixtureModel-method	posteriorSimulation-method
posterior_cases	posterior_cases
probCopyNumber	probCopyNumber
probCopyNumber,MultiBatchCopyNumber-method	probCopyNumber
probCopyNumber,MultiBatchCopyNumberPooled-method	probCopyNumber
probCopyNumber,SingleBatchCopyNumber-method	probCopyNumber
probz	probz-method
probz,MixtureModel-method	probz-method
qInverseTau2	qInverseTau2
saveBatch	saveBatch
sigma	sigma
sigma,MultiBatchCopyNumberPooled-method	sigma2-method
sigma2	sigma2-method
sigma2,BatchModel-method	Deprecated-functions
sigma2,MarginalModel-method	Deprecated-functions
sigma2,McmcChains-method	sigma2-method
sigma2,missing-method	sigma2-method
sigma2,MultiBatchModel-method	sigma2-method
sigma2,MultiBatchPooled-method	sigma2-method
sigma2,SingleBatchModel-method	sigma2-method
sigma2.0	sigma2.0-method
sigma2.0,McmcChains-method	sigma2.0-method
sigma2.0,MixtureModel-method	sigma2.0-method
sigmac	sigmac
simulateBatchData	simulateBatchData
simulateData	simulateData
SingleBatchCopyNumber	CopyNumber-methods
SingleBatchModel	Deprecated-functions
SingleBatchModel-class	SingleBatchModel-class
SingleBatchModel2	SingleBatchModel2
SingleBatchModelExample	SingleBatchModelExample
SingleBatchPooled	SingleBatchModel2
tau	tau
tau2	tau2-method
tau2,BatchModel-method	Deprecated-functions
tau2,MarginalModel-method	Deprecated-functions
tau2,McmcChains-method	tau2-method
tau2,MultiBatchModel-method	tau2-method
tau2,SingleBatchModel-method	tau2-method
tauc	tauc
tauMean	tauMean
theta	theta-method
theta,BatchModel-method	Deprecated-functions
theta,MarginalModel-method	Deprecated-functions
theta,McmcChains-method	theta-method
theta,MultiBatchModel-method	theta-method
theta,SingleBatchModel-method	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
upSample	tile-functions
upSample,MixtureModel-method	tile-functions
upSample,MultiBatchModel-method	tile-functions
y	y-method
y,DensityModel-method	Deprecated-functions
y,MixtureModel-method	y-method
z	z-method
z,McmcChains-method	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
[,BatchModel,ANY,ANY,ANY-method	Deprecated-functions
[,BatchModel,ANY,ANY-method	Deprecated-functions
[,BatchModel,ANY-method	Deprecated-functions
[,BatchModel-method	Deprecated-functions
[,McmcChains,ANY,ANY,ANY-method	extract-methods
[,McmcChains,ANY-method	extract-methods
[,McmcChains-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
