Bayesian mixture models for copy number polymorphisms

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Documentation for package ‘CNPBayes’ version 1.6.1

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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