Man pages for CNPBayes
Bayesian mixture models for copy number polymorphisms
| bafLikelihood | Calculate the likelihood of the observed B allele frequencies... |
| batch-method | Retrieve batches from object. |
| BatchModelExample | This data is a simulated example of Batch data |
| bayesFactor | Compute the Bayes factor |
| bic-method | Calculate BIC of a model |
| burnin-method | Number of burnin iterations. |
| chains-method | Retrieve simulated chains from model object. |
| chromosome | Extract character vector of sequence names |
| CNPBayes | Bayesian mixture models for copy number estimation |
| collapseBatch-method | Estimate batch from any sample-level surrogate variables that... |
| consensusCNP | Identify consensus start and stop coordinates of a copy... |
| copyNumber | Extract copy number estimates from a 'CopyNumberModel' |
| CopyNumber-classes | Mixture model container where mixture components have been... |
| CopyNumber-methods | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models |
| Defunct-classes | Defunct classes in CNPBayes |
| dfr-method | Accessor for degrees of freedom |
| downSample | Down sample the observations in a mixture |
| eta.0-method | Retrieve the rate parameter for the tau2 distribution. |
| extract-methods | extract estimated parameters at particular iteration of... |
| findSurrogates-MultiBatch-method | Estimate batch from any sample-level surrogate variables that... |
| ggplot-functions | Trace plots of MCMC chains and mixture model densities |
| gibbs | Run a Gibbs sampler on one or multiple types of Bayesian... |
| Hyperparameters | Create an object of class 'Hyperparameters' |
| HyperparametersBatch-class | An object to specify the hyperparameters of a batch effect... |
| Hyperparameters-class | An object to specify the hyperparameters of a model. |
| HyperparametersMarginal-class | An object to specify the hyperparameters of a marginal model. |
| HyperparametersMultiBatch | Create an object of class 'HyperparametersMultiBatch' for the... |
| HyperparametersMultiBatch-class | An object to specify the hyperparameters of a batch effect... |
| HyperparametersSingleBatch | Create an object of class 'HyperparametersSingleBatch' for... |
| HyperparametersSingleBatch-class | An object to specify the hyperparameters of a marginal model. |
| HyperparametersTrios | Create an object of class 'Hyperparameters' with additional... |
| HyperparametersTrios-class | An object to specify the hyperparameters of a model with... |
| hyperParams-method | Accessor for Hyperparameters object for a... |
| iter-method | Reset number of iterations. |
| k-method | Number of components. |
| label_switch | Accessor for determing whether label switching occurred... |
| logBayesFactor | Compute the log bayes factor between models. |
| log_lik-method | Retrieve log likelihood. |
| logPrior-method | Calculate log likelihood of prior for model |
| m2.0-method | Retrieve the shape parameter for the tau2 distribution. |
| mapCnProbability | Probabiliistic copy number assigments. |
| mapParams | Parameters for mapping mixture components to distinct copy... |
| mapping | Map mixture components to copy number states |
| map_z | Calculate the maximum a posteriori estimate of latent... |
| marginal_lik | Accessor for the log marginal likelihood of a SB, SBP, MB, or... |
| marginalLik | Extract marginal likelihoods from a list of models |
| marginalLikelihood-method | Compute the marginal likelihood of a converged model. |
| MarginalModelExample | This data is a simulated example of Marginal data |
| MBP | Constructor for MultiBatchPooled model |
| McmcChains-class | An object to hold estimated paraeters. |
| McmcParams | Create an object of class 'McmcParams' to specify iterations,... |
| McmcParams-class | An object to specify MCMC options for a later simulation |
| mcmcParams-method | Retrieve MCMC parameters from model. |
| MixtureModel-class | An object for running MCMC simulations. |
| mlParams | Parameters for evaluating marginal likelihood |
| modelName-MixtureModel-method | Abbreviated model name |
| modes-method | Retrieve the modes from a model. |
| muc | Retrieve overall mean at each iteration of the MCMC. |
| MultiBatch-class | An object for running MCMC simulations. |
| MultiBatchModel | Constructor for MultiBatchModel |
| MultiBatchModel-class | An object for running MCMC simulations. |
| MultiBatchModelExample | This data is an instance of MultiBatchModel |
| MultiBatchPooledExample | This data is an instance of MultiBatchPooled |
| muMean | Retrieve overall mean averaged across MCMC simulations. |
| mu-method | Retrieve overall mean |
| names-methods | Retrieve the names of the parameters estimated in the MCMC... |
| nStarts-method | Number of MCMC chains. |
| nu.0-method | Retrieve the shape parameter for the sigma.2 distribution. |
| numberObs-method | Number of observations |
| oned-method | Retrieve data. |
| orderModels | Order models by Bayes factor |
| pic | Retrieve mixture proportions at each iteration of the MCMC. |
| p-MixtureModel-method | Retrieve mixture proportions. |
| posterior_cases | Calculate posterior proportion of cases by component |
| posteriorPredictive | Simulate data from the posterior predictive distribution |
| posteriorSimulation-method | Run MCMC simulation. |
| pp | Retrieve mixture proportions of parents. |
| probCopyNumber | Posterior probabilities for copy number states |
| probz-method | Retrieve the probability of latent variable membership by... |
| probzpar-method | Retrieve the probability of latent variable membership by... |
| qInverseTau2 | Quantiles, shape, and rate of the prior for the inverse of... |
| saveBatch | Save se data |
| sigma | Retrieve standard deviations of each component/batch mean. |
| sigma2.0-method | Retrieve the rate parameter for the sigma.2 distribution. |
| sigma2-method | Retrieve the variances of each component and batch... |
| sigmac | Retrieve standard deviation of each component/batch mean at... |
| simulateBatchData | Create simulated batch data for testing. |
| simulateData | Create simulated data for testing. |
| singleBatchGuided-MultiBatchList-MultiBatch-method | Use values from SingleBatch model to simulate reasonable... |
| SingleBatchModel | Constructors for SB and SBP models |
| SingleBatchModel-class | The 'SingleBatchModel' class |
| SingleBatchModelExample | This data is an instance of SingleBatchModel |
| tau | Retrieve overall standard deviation. |
| tau2-method | Accessor for the tau2 parameter in the hierarchical mixture... |
| tauc | Retrieve overall standard deviation at each iteration of the... |
| tauMean | Retrieve overall standard deviation averaged across MCMC... |
| theta-method | Accessor for the theta parameter in the hierarchical mixture... |
| thin-method | Get or set the number of thinning intervals. |
| tile-functions | Create tile labels for each observation |
| TrioBatchModel | Constructor for TrioBatchModel |
| triodata_lrr-method | Retrieves intensity data from trios |
| upSample2 | Restore model of down-sampled to original dimension. |
| y-method | Retrieve data. |
| zfreq-method | Calculates a frequency table of latent variable assigments by... |
| zfreqpar-method | Calculates a frequency table of latent variable assigments... |
| z-method | Retrieve latent variable assignments. |
