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. |