| 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 any sample-level surrogate variables that capture aspects of sample processing, such as the PCR experiment (e.g., the 96 well chemistry plate), laboratory, DNA source, or DNA extraction method. |
| collapseBatch-method |
Estimate batch from any sample-level surrogate variables that capture aspects of sample processing, such as the PCR experiment (e.g., the 96 well chemistry plate), laboratory, DNA source, or DNA extraction method. |
| 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 |
| 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-method |
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. |
| MultiBatch-class |
An object for running MCMC simulations. |
| 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. |
| p-method |
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 |
| pp |
Retrieve mixture proportions of parents. |
| 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. |
| probzpar |
Retrieve the probability of latent variable membership by observation for parents. |
| probzpar-method |
Retrieve the probability of latent variable membership by observation for parents. |
| 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. |
| sigma2<--method |
Retrieve the variances of each component and batch distribution |
| sigma<- |
Retrieve the variances of each component and batch distribution |
| sigma<--method |
Retrieve the variances of each component and batch distribution |
| sigmac |
Retrieve standard deviation of each component/batch mean at each iteration of the MCMC. |
| sigma_-method |
Retrieve the variances of each component and batch distribution |
| 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 |
| singleBatchGuided-method |
Use values from SingleBatch model to simulate reasonable starting values for the SingleBatch-pooled and MultiBatch models of the same number of components |
| 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 |
| theta<- |
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 |
| TrioBatchModel |
Constructor for TrioBatchModel |
| triodata_lrr |
Retrieves intensity data from trios |