Bayesian mixture models for copy number polymorphisms


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Documentation for package ‘CNPBayes’ version 1.13.5

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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.