# Bayesian mixture models for copy number polymorphisms

## Documentation for package ‘CNPBayes’ version 1.4.0

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

## Help Pages

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

CNPBayes-package | Bayesian mixture models for copy number estimation

## -- B --

batch | Retrieve batches from object.
batch-method | Retrieve batches from object.
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
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
clusters | Accessor for extracting the kmeans clusters from a DensityModel instance
clusters-method | Accessor for extracting the kmeans clusters from a DensityModel instance
CNPBayes | Bayesian mixture models for copy number estimation
collapseBatch | Estimate batch from a collection of chemistry plates or some other variable that captures the time in which the arrays were processed.
collapseBatch-method | 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

## -- D --

DensityBatchModel-class | An object to store estimated mixture model densities
DensityModel | Constructor for DensityModel class
DensityModel-class | An object to store estimated mixture model densities
downsample | Create tile labels for each observation
downSampleEachBatch | Create tile labels for each observation

## -- E --

eta.0 | Retrieve the rate parameter for the tau2 distribution.
eta.0-method | Retrieve the rate parameter for the tau2 distribution.
extract | extract data, latent variable, and batch for given observation

## -- H --

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.
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 --

labelSwitching | Calculate proportion of relabeling instances
labelSwitching-method | Calculate proportion of relabeling instances
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.
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.
marginalLikelihood-method | Compute the marginal likelihood of a converged 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 | 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.
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.
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.

## -- O --

oned | Retrieve data.
oned-method | Retrieve data.

## -- P --

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
plot-method | Plot the densities estimated from a mixture model for a copy number polymorphism
posteriorSimulation | Run the MCMC simulation.
posteriorSimulation-method | Run the MCMC simulation.
posterior_cases | Calculate posterior proportion of cases by component
probz | Retrieve the probability of latent variable membership by observation.
probz-method | Retrieve the probability of latent variable membership by observation.

## -- Q --

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

## -- S --

saveBatch | Save se data
sigma | Retrieve standard deviations of each component/batch mean.
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.
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.

## -- 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
thin | Number of thinning intervals.
thin-method | Number of thinning intervals.
tracePlot | Create a trace plot of a parameter estimated by MCMC.
tracePlot-method | Create a trace plot of a parameter estimated by MCMC.

## -- 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.

## -- misc --

[-method | extract data, latent variable, and batch for given observation