Bayesian mixture models for copy number polymorphisms

batch-method | Retrieve batches from object. |

BatchModelExample | This data is a simulated example of Batch data |

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 a collection of chemistry plates or some... |

combinePlates-method | Combine chemistry plates into batches |

consensusCNP | Identify consensus start and stop coordinates of a copy... |

copyNumber | Extract copy number estimates from a 'CopyNumberModel' |

CopyNumber-methods | Constructs a CopyNumberModel from SB, SBP, MB, or MBP models |

Deprecated-classes | Deprecated classes in CNPBayes |

Deprecated-functions | DensityModel constructor has been deprecated. |

eta.0-method | Retrieve the rate parameter for the tau2 distribution. |

extract-methods | extract estimated parameters at particular iteration of... |

ggplot-functions | Trace plots of MCMC chains and mixture model densities |

ggPredictive | Compare the posterior predictive distribution to the... |

gibbs | Run a Gibbs sampler on one or multiple types of Bayesian... |

gibbs_all | Evaluate both single-batch and multi-batch models with the... |

gibbs_pooled | Evaluate both single-batch and multi-batch models with the... |

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. |

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. |

mapComponents | Map mixture components to distinct copy number states |

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... |

marginalLikelihood-method | Compute the marginal likelihood of a converged model. |

MarginalModelExample | This data is a simulated example of Marginal data |

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 |

modes-method | Retrieve the modes from a model. |

muc | Retrieve overall mean at each iteration of the MCMC. |

MultiBatchModel2 | 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. |

p | Retrieve mixture proportions. |

pic | Retrieve mixture proportions at each iteration of the MCMC. |

posterior_cases | Calculate posterior proportion of cases by component |

posteriorPredictive | Simulate data from the posterior predictive distribution |

posteriorSimulation-method | Run MCMC simulation. |

probCopyNumber | Posterior probabilities for copy number states |

probz-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. |

SingleBatchModel2 | 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 |

y-method | Retrieve data. |

zfreq-method | Calculates a frequency table of latent variable assigments by... |

z-method | Retrieve latent variable assignments. |

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