Bayesian mixture models for copy number polymorphisms


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Documentation for package ‘CNPBayes’ version 1.10.0

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B C D E 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 --

batch Retrieve batches from object.
batch-method DensityModel constructor has been deprecated.
batch-method Retrieve batches from object.
BatchModel DensityModel constructor has been deprecated.
BatchModel-class Deprecated classes in CNPBayes
BatchModelExample This data is a simulated example of Batch data
BatchModelList DensityModel constructor has been deprecated.
bic Calculate BIC of a model
bic-method DensityModel constructor has been deprecated.
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 DensityModel constructor has been deprecated.
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.
combinePlates Combine chemistry plates into batches
combinePlates-method Combine chemistry plates into batches
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 Deprecated classes in CNPBayes
DensityModel DensityModel constructor has been deprecated.
DensityModel-class Deprecated classes in CNPBayes
downsample DensityModel constructor has been deprecated.
downSampleEachBatch DensityModel constructor has been deprecated.

-- 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.

-- 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
ggMultiBatch Trace plots of MCMC chains and mixture model densities
ggMultiBatch-method DensityModel constructor has been deprecated.
ggPredictive Compare the posterior predictive distribution to the empirical data
ggSingleBatch Trace plots of MCMC chains and mixture model densities
ggSingleBatch-method DensityModel constructor has been deprecated.
ggSingleBatchChains Trace plots of MCMC chains and mixture model densities
gibbs Run a Gibbs sampler on one or multiple types of Bayesian Gaussian mixture models
gibbs_all Evaluate both single-batch and multi-batch models with the specified range for the number of components, returning the top models sorted by marginal likelihood
gibbs_pooled Evaluate both single-batch and multi-batch models with the specified range for the number of components, returning the top models sorted by marginal likelihood

-- 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 DensityModel constructor has been deprecated.
HyperparametersBatch-class An object to specify the hyperparameters of a batch effect model.
HyperparametersMarginal DensityModel constructor has been deprecated.
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.
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 DensityModel constructor has been deprecated.
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 DensityModel constructor has been deprecated.
labelSwitching-method DensityModel constructor has been deprecated.
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.
mapComponents Map mixture components to distinct copy number states
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.
marginalLikelihood Compute the marginal likelihood of a converged model.
marginalLikelihood-method DensityModel constructor has been deprecated.
marginalLikelihood-method Compute the marginal likelihood of a converged model.
MarginalModel-class Deprecated 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
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
modes Retrieve the modes from a model.
modes-method DensityModel constructor has been deprecated.
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.
MultiBatchCopyNumber Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
MultiBatchCopyNumberPooled Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
multiBatchDensities DensityModel constructor has been deprecated.
MultiBatchModel DensityModel constructor has been deprecated.
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.

-- P --

p Retrieve mixture proportions.
pic Retrieve mixture proportions at each iteration of the MCMC.
plot DensityModel constructor has been deprecated.
plot-method DensityModel constructor has been deprecated.
posteriorPredictive Simulate data from the posterior predictive distribution
posteriorSimulation Run MCMC simulation.
posteriorSimulation-method DensityModel constructor has been deprecated.
posteriorSimulation-method Run MCMC simulation.
posterior_cases Calculate posterior proportion of cases by component
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.

-- 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.
sigma-method Retrieve the variances of each component and batch distribution
sigma2 Retrieve the variances of each component and batch distribution
sigma2-method DensityModel constructor has been deprecated.
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.
SingleBatchCopyNumber Constructs a CopyNumberModel from SB, SBP, MB, or MBP models
SingleBatchModel DensityModel constructor has been deprecated.
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 DensityModel constructor has been deprecated.
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 DensityModel constructor has been deprecated.
theta-method 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

-- U --

upSample Create tile labels for each observation
upSample-method Create tile labels for each observation

-- Y --

y Retrieve data.
y-method DensityModel constructor has been deprecated.
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 DensityModel constructor has been deprecated.
[-method extract estimated parameters at particular iteration of simulation.