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 |
| 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. |
| 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 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. |
| 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 |
| 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 |
| 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. |
| 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 |
| 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. |
| 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 |
| 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 | 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. |
| 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. |
| 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 | 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. |
| 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. |
| 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 |
| oned | Retrieve data. |
| oned-method | Retrieve data. |
| orderModels | Order models by Bayes factor |
| p | 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 |
| 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. |
| qInverseTau2 | Quantiles, shape, and rate of the prior for the inverse of tau2 (the precision) |
| 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. |
| 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 |
| SingleBatchCopyNumber-class | Mixture model container where mixture components have been genotyped |
| 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 |
| 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 |
| 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 |
| upSample2 | Restore model of down-sampled to original dimension. |
| y | Retrieve data. |
| y-method | Retrieve data. |
| 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. |
| [-method | extract estimated parameters at particular iteration of simulation. |