Man pages for CNPBayes
Bayesian mixture models for copy number polymorphisms

batch-methodRetrieve batches from object.
BatchModelExampleThis data is a simulated example of Batch data
bic-methodCalculate BIC of a model
burnin-methodNumber of burnin iterations.
chains-methodRetrieve simulated chains from model object.
chromosomeExtract character vector of sequence names
CNPBayesBayesian mixture models for copy number estimation
collapseBatch-methodEstimate batch from a collection of chemistry plates or some...
combinePlates-methodCombine chemistry plates into batches
consensusCNPIdentify consensus start and stop coordinates of a copy...
copyNumberExtract copy number estimates from a 'CopyNumberModel'
CopyNumber-methodsConstructs a CopyNumberModel from SB, SBP, MB, or MBP models
Deprecated-classesDeprecated classes in CNPBayes
Deprecated-functionsDensityModel constructor has been deprecated.
eta.0-methodRetrieve the rate parameter for the tau2 distribution.
extract-methodsextract estimated parameters at particular iteration of...
ggplot-functionsTrace plots of MCMC chains and mixture model densities
ggPredictiveCompare the posterior predictive distribution to the...
gibbsRun a Gibbs sampler on one or multiple types of Bayesian...
gibbs_allEvaluate both single-batch and multi-batch models with the...
gibbs_pooledEvaluate both single-batch and multi-batch models with the...
HyperparametersCreate an object of class 'Hyperparameters'
HyperparametersBatch-classAn object to specify the hyperparameters of a batch effect...
Hyperparameters-classAn object to specify the hyperparameters of a model.
HyperparametersMarginal-classAn object to specify the hyperparameters of a marginal model.
HyperparametersMultiBatchCreate an object of class 'HyperparametersMultiBatch' for the...
HyperparametersMultiBatch-classAn object to specify the hyperparameters of a batch effect...
HyperparametersSingleBatchCreate an object of class 'HyperparametersSingleBatch' for...
HyperparametersSingleBatch-classAn object to specify the hyperparameters of a marginal model.
hyperParams-methodAccessor for Hyperparameters object for a...
iter-methodReset number of iterations.
k-methodNumber of components.
label_switchAccessor for determing whether label switching occurred...
logBayesFactorCompute the log bayes factor between models.
log_lik-methodRetrieve log likelihood.
logPrior-methodCalculate log likelihood of prior for model
m2.0-methodRetrieve the shape parameter for the tau2 distribution.
mapCnProbabilityProbabiliistic copy number assigments.
mapComponentsMap mixture components to distinct copy number states
mapParamsParameters for mapping mixture components to distinct copy...
mappingMap mixture components to copy number states
map_zCalculate the maximum a posteriori estimate of latent...
marginal_likAccessor for the log marginal likelihood of a SB, SBP, MB, or...
marginalLikelihood-methodCompute the marginal likelihood of a converged model.
MarginalModelExampleThis data is a simulated example of Marginal data
McmcChains-classAn object to hold estimated paraeters.
McmcParamsCreate an object of class 'McmcParams' to specify iterations,...
McmcParams-classAn object to specify MCMC options for a later simulation
mcmcParams-methodRetrieve MCMC parameters from model.
MixtureModel-classAn object for running MCMC simulations.
mlParamsParameters for evaluating marginal likelihood
modes-methodRetrieve the modes from a model.
mucRetrieve overall mean at each iteration of the MCMC.
MultiBatchModel2Constructor for MultiBatchModel
MultiBatchModel-classAn object for running MCMC simulations.
MultiBatchModelExampleThis data is an instance of MultiBatchModel
MultiBatchPooledExampleThis data is an instance of MultiBatchPooled
muMeanRetrieve overall mean averaged across MCMC simulations.
mu-methodRetrieve overall mean
names-methodsRetrieve the names of the parameters estimated in the MCMC...
nStarts-methodNumber of MCMC chains.
nu.0-methodRetrieve the shape parameter for the sigma.2 distribution.
numberObs-methodNumber of observations
oned-methodRetrieve data.
pRetrieve mixture proportions.
picRetrieve mixture proportions at each iteration of the MCMC.
posterior_casesCalculate posterior proportion of cases by component
posteriorPredictiveSimulate data from the posterior predictive distribution
posteriorSimulation-methodRun MCMC simulation.
probCopyNumberPosterior probabilities for copy number states
probz-methodRetrieve the probability of latent variable membership by...
qInverseTau2Quantiles, shape, and rate of the prior for the inverse of...
saveBatchSave se data
sigmaRetrieve standard deviations of each component/batch mean.
sigma2.0-methodRetrieve the rate parameter for the sigma.2 distribution.
sigma2-methodRetrieve the variances of each component and batch...
sigmacRetrieve standard deviation of each component/batch mean at...
simulateBatchDataCreate simulated batch data for testing.
simulateDataCreate simulated data for testing.
SingleBatchModel2Constructors for SB and SBP models
SingleBatchModel-classThe 'SingleBatchModel' class
SingleBatchModelExampleThis data is an instance of SingleBatchModel
tauRetrieve overall standard deviation.
tau2-methodAccessor for the tau2 parameter in the hierarchical mixture...
taucRetrieve overall standard deviation at each iteration of the...
tauMeanRetrieve overall standard deviation averaged across MCMC...
theta-methodAccessor for the theta parameter in the hierarchical mixture...
thin-methodGet or set the number of thinning intervals.
tile-functionsCreate tile labels for each observation
y-methodRetrieve data.
zfreq-methodCalculates a frequency table of latent variable assigments by...
z-methodRetrieve latent variable assignments.
CNPBayes documentation built on May 2, 2018, 3:57 a.m.