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      Defunct 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.
HyperparametersTrios    Create an object of class 'Hyperparameters'
                        with additional parameters for Trios
HyperparametersTrios-class
                        An object to specify the hyperparameters of a
                        model with additional parameters for trios
MBP                     Constructor for MultiBatchPooled 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.
MultiBatch-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
SingleBatchCopyNumber-class
                        Mixture model container where mixture
                        components have been genotyped
SingleBatchModel-class
                        The 'SingleBatchModel' class
SingleBatchModel2       Constructors for SB and SBP models
SingleBatchModelExample
                        This data is an instance of SingleBatchModel
TrioBatchModel          Constructor for TrioBatchModel
[,McmcChains,ANY,ANY,ANY-method
                        extract estimated parameters at particular
                        iteration of simulation.
bafLikelihood           Calculate the likelihood of the observed B
                        allele frequencies for a given copy number
                        model
batch                   Retrieve batches from object.
bayesFactor             Compute the Bayes factor
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 any sample-level surrogate
                        variables that capture aspects of sample
                        processing, such as the PCR experiment (e.g.,
                        the 96 well chemistry plate), laboratory, DNA
                        source, or DNA extraction method.
consensusCNP            Identify consensus start and stop coordinates
                        of a copy number polymorphism
copyNumber              Extract copy number estimates from a
                        'CopyNumberModel'
dfr                     Accessor for degrees of freedom
downSample              Down sample the observations in a mixture
eta.0                   Retrieve the rate parameter for the tau2
                        distribution.
findSurrogates,MultiBatch-method
                        Estimate batch from any sample-level surrogate
                        variables that capture aspects of sample
                        processing, such as the PCR experiment (e.g.,
                        the 96 well chemistry plate), laboratory, DNA
                        source, or DNA extraction method.
ggChains                Trace plots of MCMC chains and mixture model
                        densities
gibbs                   Run a Gibbs sampler on one or multiple types of
                        Bayesian Gaussian mixture models
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.
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
marginalLik             Extract marginal likelihoods from a list of
                        models
marginalLikelihood      Compute the marginal likelihood of a converged
                        model.
marginal_lik            Accessor for the log marginal likelihood of a
                        SB, SBP, MB, or MBP model
mcmcParams              Retrieve MCMC parameters from model.
mlParams                Parameters for evaluating marginal likelihood
modelName,MixtureModel-method
                        Abbreviated model name
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.
orderModels             Order models by Bayes factor
p,MixtureModel-method   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
pp                      Retrieve mixture proportions of parents.
probCopyNumber          Posterior probabilities for copy number states
probz                   Retrieve the probability of latent variable
                        membership by observation.
probzpar                Retrieve the probability of latent variable
                        membership by observation for parents.
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.
sigma2.0                Retrieve the rate parameter for the sigma.2
                        distribution.
sigma<-                 Retrieve the variances of each component and
                        batch 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.
singleBatchGuided,MultiBatchList,MultiBatch-method
                        Use values from SingleBatch model to simulate
                        reasonable starting values for the
                        SingleBatch-pooled and MultiBatch models of the
                        same number of components
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                    Get or set the number of thinning intervals.
tileMedians             Create tile labels for each observation
triodata_lrr            Retrieves intensity data from trios
upSample2               Restore model of down-sampled to original
                        dimension.
y                       Retrieve data.
z                       Retrieve latent variable assignments.
zFreq                   Calculates a frequency table of latent variable
                        assigments by observation.
zFreqPar                Calculates a frequency table of latent variable
                        assigments for parents by observation.
