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 |