BatchModelExample       This data is a simulated example of Batch data
CNPBayes                Bayesian mixture models for copy number
                        estimation
CopyNumberModel         Constructs a CopyNumberModel from SB, SBP, MB,
                        or MBP models
DensityModel-class      Deprecated classes in CNPBayes
Hyperparameters         Create an object of class 'Hyperparameters'
Hyperparameters-class   An object to specify the hyperparameters of a
                        model.
HyperparametersBatch-class
                        An object to specify the hyperparameters of a
                        batch effect model.
HyperparametersMarginal-class
                        An object to specify the hyperparameters of a
                        marginal model.
HyperparametersMultiBatch
                        Create an object of class
                        'HyperparametersMultiBatch' for the batch
                        mixture model
HyperparametersMultiBatch-class
                        An object to specify the hyperparameters of a
                        batch effect model.
HyperparametersSingleBatch
                        Create an object of class
                        'HyperparametersSingleBatch' for the single
                        batch mixture model
HyperparametersSingleBatch-class
                        An object to specify the hyperparameters of a
                        marginal model.
MarginalModelExample    This data is a simulated example of Marginal
                        data
McmcChains-class        An object to hold estimated paraeters.
McmcParams              Create an object of class 'McmcParams' to
                        specify iterations, burnin, etc.
McmcParams-class        An object to specify MCMC options for a later
                        simulation
MixtureModel-class      An object for running MCMC simulations.
MultiBatchModel-class   An object for running MCMC simulations.
MultiBatchModel2        Constructor for MultiBatchModel
MultiBatchModelExample
                        This data is an instance of MultiBatchModel
MultiBatchPooledExample
                        This data is an instance of MultiBatchPooled
SingleBatchModel-class
                        The 'SingleBatchModel' class
SingleBatchModel2       Constructors for SB and SBP models
SingleBatchModelExample
                        This data is an instance of SingleBatchModel
[,McmcChains,ANY,ANY,ANY-method
                        extract estimated parameters at particular
                        iteration of simulation.
batch                   Retrieve batches from object.
bic                     Calculate BIC of a model
burnin                  Number of burnin iterations.
chains                  Retrieve simulated chains from model object.
chromosome              Extract character vector of sequence names
collapseBatch           Estimate batch from a collection of chemistry
                        plates or some other variable that captures the
                        time in which the arrays were processed.
combinePlates           Combine chemistry plates into batches
consensusCNP            Identify consensus start and stop coordinates
                        of a copy number polymorphism
copyNumber              Extract copy number estimates from a
                        'CopyNumberModel'
eta.0                   Retrieve the rate parameter for the tau2
                        distribution.
ggChains                Trace plots of MCMC chains and mixture model
                        densities
ggPredictive            Compare the posterior predictive distribution
                        to the empirical data
gibbs                   Run a Gibbs sampler on one or multiple types of
                        Bayesian Gaussian mixture models
gibbs_all               Evaluate both single-batch and multi-batch
                        models with the specified range for the number
                        of components, returning the top models sorted
                        by marginal likelihood
gibbs_pooled            Evaluate both single-batch and multi-batch
                        models with the specified range for the number
                        of components, returning the top models sorted
                        by marginal likelihood
hyperParams             Accessor for Hyperparameters object for a
                        MixtureModel-derived object
iter<-                  Reset number of iterations.
k                       Number of components.
label_switch            Accessor for determing whether label switching
                        occurred during MCMC
logBayesFactor          Compute the log bayes factor between models.
logPrior                Calculate log likelihood of prior for model
log_lik                 Retrieve log likelihood.
m2.0                    Retrieve the shape parameter for the tau2
                        distribution.
mapCnProbability        Probabiliistic copy number assigments.
mapComponents           Map mixture components to distinct copy number
                        states
mapParams               Parameters for mapping mixture components to
                        distinct copy number states
map_z                   Calculate the maximum a posteriori estimate of
                        latent variable assignment.
mapping                 Map mixture components to copy number states
marginalLikelihood      Compute the marginal likelihood of a converged
                        model.
marginal_lik            Accessor for marginal likelihood
mcmcParams              Retrieve MCMC parameters from model.
mlParams                Parameters for evaluating marginal likelihood
modes                   Retrieve the modes from a model.
mu                      Retrieve overall mean
muMean                  Retrieve overall mean averaged across MCMC
                        simulations.
muc                     Retrieve overall mean at each iteration of the
                        MCMC.
nStarts                 Number of MCMC chains.
names,McmcChains-method
                        Retrieve the names of the parameters estimated
                        in the MCMC chain.
nu.0                    Retrieve the shape parameter for the sigma.2
                        distribution.
numberObs               Number of observations
oned                    Retrieve data.
p                       Retrieve mixture proportions.
pic                     Retrieve mixture proportions at each iteration
                        of the MCMC.
posteriorPredictive     Simulate data from the posterior predictive
                        distribution
posteriorSimulation     Run MCMC simulation.
posterior_cases         Calculate posterior proportion of cases by
                        component
probCopyNumber          Posterior probabilities for copy number states
probz                   Retrieve the probability of latent variable
                        membership by observation.
qInverseTau2            Quantiles, shape, and rate of the prior for the
                        inverse of tau2 (the precision)
saveBatch               Save se data
sigma                   Retrieve standard deviations of each
                        component/batch mean.
sigma2                  Retrieve the variances of each component and
                        batch distribution
sigma2.0                Retrieve the rate parameter for the sigma.2
                        distribution.
sigmac                  Retrieve standard deviation of each
                        component/batch mean at each iteration of the
                        MCMC.
simulateBatchData       Create simulated batch data for testing.
simulateData            Create simulated data for testing.
tau                     Retrieve overall standard deviation.
tau2                    Accessor for the tau2 parameter in the
                        hierarchical mixture model
tau2,MarginalModel-method
                        DensityModel constructor has been deprecated.
tauMean                 Retrieve overall standard deviation averaged
                        across MCMC simulations.
tauc                    Retrieve overall standard deviation at each
                        iteration of the MCMC.
theta                   Accessor for the theta parameter in the
                        hierarchical mixture model
thin                    Get or set the number of thinning intervals.
upSample                Create tile labels for each observation
y                       Retrieve data.
z                       Retrieve latent variable assignments.
zFreq                   Calculates a frequency table of latent variable
                        assigments by observation.
