Man pages for CNPBayes
Bayesian mixture models for copy number polymorphisms

bafLikelihoodCalculate the likelihood of the observed B allele frequencies...
batch-methodRetrieve batches from object.
BatchModelExampleThis data is a simulated example of Batch data
bayesFactorCompute the Bayes factor
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...
consensusCNPIdentify consensus start and stop coordinates of a copy...
copyNumberExtract copy number estimates from a 'CopyNumberModel'
CopyNumber-classesMixture model container where mixture components have been...
CopyNumber-methodsConstructs a CopyNumberModel from SB, SBP, MB, or MBP models
Defunct-classesDefunct classes in CNPBayes
dfr-methodAccessor for degrees of freedom
downSampleDown sample the observations in a mixture
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
gibbsRun a Gibbs sampler on one or multiple types of Bayesian...
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.
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...
marginalLikExtract marginal likelihoods from a list of models
marginalLikelihood-methodCompute the marginal likelihood of a converged model.
MarginalModelExampleThis data is a simulated example of Marginal data
MBConstructor for MultiBatchModel
MBPConstructor for MultiBatchPooled model
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
modelNameAbbreviated model name
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.
orderModelsOrder models by Bayes factor
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.
SingleBatchModelConstructors 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
upSample2Restore model of down-sampled to original dimension.
y-methodRetrieve data.
zfreq-methodCalculates a frequency table of latent variable assigments by...
z-methodRetrieve latent variable assignments.
CNPBayes documentation built on Nov. 1, 2018, 4:47 a.m.