# Bayesian mixture models for copy number polymorphisms

## Documentation for package ‘CNPBayes’ version 1.13.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C D E F G H I K L M N O P Q S T U Y Z misc

CNPBayes-package | Bayesian mixture models for copy number estimation

## -- B --

bafLikelihood | Calculate the likelihood of the observed B allele frequencies for a given copy number model
batch | Retrieve batches from object.
batch-method | Retrieve batches from object.
BatchModel-class | Defunct classes in CNPBayes
BatchModelExample | This data is a simulated example of Batch data
bayesFactor | Compute the Bayes factor
bic | Calculate BIC of a model
bic-method | Calculate BIC of a model
burnin | Number of burnin iterations.
burnin-method | Number of burnin iterations.
burnin<- | Number of burnin iterations.
burnin<--method | Number of burnin iterations.

## -- C --

chains | Retrieve simulated chains from model object.
chains-method | Retrieve simulated chains from model object.
chromosome | Extract character vector of sequence names
chromosome-method | Extract character vector of sequence names
CNPBayes | Bayesian mixture models for copy number estimation
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.
collapseBatch-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.
consensusCNP | Identify consensus start and stop coordinates of a copy number polymorphism
copyNumber | Extract copy number estimates from a 'CopyNumberModel'
copyNumber-method | Extract copy number estimates from a 'CopyNumberModel'
CopyNumberModel | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
CopyNumberModel-method | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models

## -- D --

DensityBatchModel-class | Defunct classes in CNPBayes
DensityModel-class | Defunct classes in CNPBayes
dfr | Accessor for degrees of freedom
dfr-method | Accessor for degrees of freedom
dfr<- | Accessor for degrees of freedom
dfr<--method | Accessor for degrees of freedom
downSample | Down sample the observations in a mixture

## -- E --

eta.0 | Retrieve the rate parameter for the tau2 distribution.
eta.0-method | Retrieve the rate parameter for the tau2 distribution.
extract | extract estimated parameters at particular iteration of simulation.

## -- F --

findSurrogates-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.

## -- G --

ggChains | Trace plots of MCMC chains and mixture model densities
ggChains-method | Trace plots of MCMC chains and mixture model densities
ggMixture | Trace plots of MCMC chains and mixture model densities
ggMixture-method | Trace plots of MCMC chains and mixture model densities
gibbs | Run a Gibbs sampler on one or multiple types of Bayesian Gaussian mixture models

## -- H --

hpList | Create an object of class 'Hyperparameters'
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
hyperParams | Accessor for Hyperparameters object for a MixtureModel-derived object
hyperParams-method | Accessor for Hyperparameters object for a MixtureModel-derived object
hyperParams<- | Accessor for Hyperparameters object for a MixtureModel-derived object
hyperParams<--method | Accessor for Hyperparameters object for a MixtureModel-derived object

## -- I --

iter | Reset number of iterations.
iter-method | An object to specify MCMC options for a later simulation
iter-method | Reset number of iterations.
iter<- | Reset number of iterations.
iter<--method | Reset number of iterations.

## -- K --

k | Number of components.
k-method | An object to specify the hyperparameters of a model.
k-method | Number of components.
k<- | Number of components.
k<--method | Number of components.

## -- L --

label_switch | Accessor for determing whether label switching occurred during MCMC
label_switch-method | 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
logPrior-method | Calculate log likelihood of prior for model
log_lik | Retrieve log likelihood.
log_lik-method | Retrieve log likelihood.

## -- M --

m2.0 | Retrieve the shape parameter for the tau2 distribution.
m2.0-method | Retrieve the shape parameter for the tau2 distribution.
mapCnProbability | Probabiliistic copy number assigments.
mapCopyNumber | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
mapParams | Parameters for mapping mixture components to distinct copy number states
mapping | Map mixture components to copy number states
mapping-method | Map mixture components to copy number states
mapping<- | Map mixture components to copy number states
mapping<--method | Map mixture components to copy number states
map_z | Calculate the maximum a posteriori estimate of latent variable assignment.
marginalLik | Extract marginal likelihoods from a list of models
marginalLikelihood | Compute the marginal likelihood of a converged model.
marginalLikelihood-method | Compute the marginal likelihood of a converged model.
MarginalModel-class | Defunct classes in CNPBayes
MarginalModelExample | This data is a simulated example of Marginal data
marginal_lik | Accessor for the log marginal likelihood of a SB, SBP, MB, or MBP model
marginal_lik-method | Accessor for the log marginal likelihood of a SB, SBP, MB, or MBP model
marginal_lik<- | Accessor for the log marginal likelihood of a SB, SBP, MB, or MBP model
marginal_lik<--method | Accessor for the log marginal likelihood of a SB, SBP, MB, or MBP model
MB | Constructor for MultiBatchModel
MBP | Constructor for MultiBatchPooled model
McmcChains-class | An object to hold estimated paraeters.
McmcParams | Create an object of class 'McmcParams' to specify iterations, burnin, etc.
mcmcParams | Retrieve MCMC parameters from model.
McmcParams-class | An object to specify MCMC options for a later simulation
mcmcParams-method | Retrieve MCMC parameters from model.
mcmcParams<- | Retrieve MCMC parameters from model.
mcmcParams<--method | Retrieve MCMC parameters from model.
MixtureModel-class | An object for running MCMC simulations.
mlParams | Parameters for evaluating marginal likelihood
modelName-method | Abbreviated model name
modes | Retrieve the modes from a model.
modes-method | Retrieve the modes from a model.
modes<- | Retrieve the modes from a model.
modes<--method | Retrieve the modes from a model.
mu | Retrieve overall mean
mu-method | Retrieve overall mean
muc | Retrieve overall mean at each iteration of the MCMC.
MultiBatch-class | An object for running MCMC simulations.
MultiBatchCopyNumber | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
MultiBatchCopyNumber-class | Mixture model container where mixture components have been genotyped
MultiBatchCopyNumberPooled | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
MultiBatchCopyNumberPooled-class | Mixture model container where mixture components have been genotyped
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
muMean | Retrieve overall mean averaged across MCMC simulations.

## -- N --

names-method | Retrieve the names of the parameters estimated in the MCMC chain.
nStarts | Number of MCMC chains.
nStarts-method | Number of MCMC chains.
nStarts<- | Number of MCMC chains.
nStarts<--method | Number of MCMC chains.
nu.0 | Retrieve the shape parameter for the sigma.2 distribution.
nu.0-method | Retrieve the shape parameter for the sigma.2 distribution.
numberObs | Number of observations
numberObs-method | Number of observations

## -- O --

oned | Retrieve data.
oned-method | Retrieve data.
orderModels | Order models by Bayes factor

## -- P --

p-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.
posteriorSimulation-method | 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
probCopyNumber-method | Posterior probabilities for copy number states
probz | Retrieve the probability of latent variable membership by observation.
probz-method | Retrieve the probability of latent variable membership by observation.
probzpar | Retrieve the probability of latent variable membership by observation for parents.
probzpar-method | Retrieve the probability of latent variable membership by observation for parents.

## -- Q --

qInverseTau2 | Quantiles, shape, and rate of the prior for the inverse of tau2 (the precision)

## -- S --

saveBatch | Save se data
SB | Constructors for SB and SBP models
SBP | Constructors for SB and SBP models
sigma | Retrieve standard deviations of each component/batch mean.
sigma-method | Retrieve the variances of each component and batch distribution
sigma2 | Retrieve the variances of each component and batch distribution
sigma2-method | Retrieve the variances of each component and batch distribution
sigma2.0 | Retrieve the rate parameter for the sigma.2 distribution.
sigma2.0-method | Retrieve the rate parameter for the sigma.2 distribution.
sigma2<--method | Retrieve the variances of each component and batch distribution
sigma<- | Retrieve the variances of each component and batch distribution
sigma<--method | Retrieve the variances of each component and batch distribution
sigmac | Retrieve standard deviation of each component/batch mean at each iteration of the MCMC.
sigma_-method | Retrieve the variances of each component and batch distribution
simulateBatchData | Create simulated batch data for testing.
simulateData | Create simulated data for testing.
SingleBatchCopyNumber | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
SingleBatchCopyNumber-class | Mixture model container where mixture components have been genotyped
singleBatchGuided-method | Use values from SingleBatch model to simulate reasonable starting values for the SingleBatch-pooled and MultiBatch models of the same number of components
SingleBatchModel-class | The 'SingleBatchModel' class
SingleBatchModel2 | Constructors for SB and SBP models
SingleBatchModelExample | This data is an instance of SingleBatchModel
SingleBatchPooled | Constructors for SB and SBP models

## -- T --

tau | Retrieve overall standard deviation.
tau2 | Accessor for the tau2 parameter in the hierarchical mixture model
tau2-method | Accessor for the tau2 parameter in the hierarchical mixture model
tauc | Retrieve overall standard deviation at each iteration of the MCMC.
tauMean | Retrieve overall standard deviation averaged across MCMC simulations.
theta | Accessor for the theta parameter in the hierarchical mixture model
theta-method | Accessor for the theta parameter in the hierarchical mixture model
theta<- | Accessor for the theta parameter in the hierarchical mixture model
thin | Get or set the number of thinning intervals.
thin-method | Get or set the number of thinning intervals.
thin<- | Get or set the number of thinning intervals.
thin<--method | Get or set the number of thinning intervals.
tileMedians | Create tile labels for each observation
tileSummaries | Create tile labels for each observation
TrioBatchModel | Constructor for TrioBatchModel
triodata_lrr | Retrieves intensity data from trios

## -- U --

upSample2 | Restore model of down-sampled to original dimension.

## -- Y --

y | Retrieve data.
y-method | Retrieve data.

## -- Z --

z | Retrieve latent variable assignments.
z-method | Retrieve latent variable assignments.
zFreq | Calculates a frequency table of latent variable assigments by observation.
zFreq-method | Calculates a frequency table of latent variable assigments by observation.
zfreq-method | Calculates a frequency table of latent variable assigments by observation.
zFreqPar | Calculates a frequency table of latent variable assigments for parents by observation.
zFreqPar-method | Calculates a frequency table of latent variable assigments for parents by observation.
zfreqpar-method | Calculates a frequency table of latent variable assigments for parents by observation.

## -- misc --

[-method | extract estimated parameters at particular iteration of simulation.