BatchModel              Create an object for running hierarchical MCMC
                        simulations.
BatchModel-class        An object for running MCMC simulations.
BatchModelExample       This data is a simulated example of Batch data
CNPBayes                Bayesian mixture models for copy number
                        estimation
DensityModel            Constructor for DensityModel class
DensityModel-class      An object to store estimated mixture model
                        densities
Hyperparameters         Create an object of class 'Hyperparameters'
Hyperparameters-class   An object to specify the hyperparameters of a
                        model.
HyperparametersBatch    Create an object of class
                        'HyperparametersBatch' for the batch mixture
                        model
HyperparametersBatch-class
                        An object to specify the hyperparameters of a
                        batch effect model.
HyperparametersMarginal
                        Create an object of class
                        'HyperparametersMarginal' for the marginal
                        mixture model
HyperparametersMarginal-class
                        An object to specify the hyperparameters of a
                        marginal model.
MarginalModel           Create an object for running marginal MCMC
                        simulations.
MarginalModel-class     The 'MarginalModel' class
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.
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
clusters                Accessor for extracting the kmeans clusters
                        from a DensityModel instance
collapseBatch           Estimate batch from a collection of chemistry
                        plates or some other variable that captures the
                        time in which the arrays were processed.
consensusCNP            Identify consensus start and stop coordinates
                        of a copy number polymorphism
downSampleEachBatch     Create tile labels for each observation
downsample              Create tile labels for each observation
eta.0                   Retrieve the rate parameter for the tau2
                        distribution.
extract                 extract data, latent variable, and batch for
                        given observation
hyperParams             Accessor for Hyperparameters object for a
                        MixtureModel-derived object
iter<-                  Reset number of iterations.
k                       Number of components.
labelSwitching          Calculate proportion of relabeling instances
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.
map                     Calculate the maximum a posteriori estimate of
                        latent variable assignment.
mapCnProbability        Probabiliistic copy number assigments.
marginalLikelihood      Compute the marginal likelihood of a converged
                        model.
mcmcParams              Retrieve MCMC parameters from model.
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.
oned                    Retrieve data.
p                       Retrieve mixture proportions.
pic                     Retrieve mixture proportions at each iteration
                        of the MCMC.
plot                    Plot the densities estimated from a mixture
                        model for a copy number polymorphism
posteriorSimulation     Run the MCMC simulation.
posterior_cases         Calculate posterior proportion of cases by
                        component
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
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                    Number of thinning intervals.
tracePlot               Create a trace plot of a parameter estimated by
                        MCMC.
y                       Retrieve data.
z                       Retrieve latent variable assignments.
zFreq                   Calculates a frequency table of latent variable
                        assigments by observation.
