B C D E H I K L M N O P Q S T Y Z misc
CNPBayes-package | Bayesian mixture models for copy number estimation |
batch | Retrieve batches from object. |
batch-method | Retrieve batches from object. |
BatchModel | Create an object for running hierarchical MCMC simulations. |
BatchModel-class | An object for running MCMC simulations. |
BatchModelExample | This data is a simulated example of Batch data |
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 |
clusters | Accessor for extracting the kmeans clusters from a DensityModel instance |
clusters-method | Accessor for extracting the kmeans clusters from a DensityModel instance |
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 |
DensityBatchModel-class | An object to store estimated mixture model densities |
DensityModel | Constructor for DensityModel class |
DensityModel-class | An object to store estimated mixture model densities |
downsample | Create tile labels for each observation |
downSampleEachBatch | Create tile labels for each observation |
eta.0 | Retrieve the rate parameter for the tau2 distribution. |
eta.0-method | Retrieve the rate parameter for the tau2 distribution. |
extract | extract data, latent variable, and batch for given observation |
Hyperparameters | Create an object of class 'Hyperparameters' |
Hyperparameters-class | An object to specify the hyperparameters of a model. |
HyperparametersBatch | Create an object of class 'HyperparametersBatch' for the batch mixture model |
HyperparametersBatch-class | An object to specify the hyperparameters of a batch effect model. |
HyperparametersMarginal | Create an object of class 'HyperparametersMarginal' for the marginal mixture model |
HyperparametersMarginal-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. |
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. |
map | Calculate the maximum a posteriori estimate of latent variable assignment. |
mapCnProbability | Probabiliistic copy number assigments. |
marginalLikelihood | Compute the marginal likelihood of a converged model. |
marginalLikelihood-method | Compute the marginal likelihood of a converged model. |
MarginalModel | Create an object for running marginal MCMC simulations. |
MarginalModel-class | The 'MarginalModel' class |
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, 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. |
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. |
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. |
oned | Retrieve data. |
oned-method | Retrieve data. |
p | Retrieve mixture proportions. |
pic | Retrieve mixture proportions at each iteration of the MCMC. |
plot | Plot the densities estimated from a mixture model for a copy number polymorphism |
plot-method | Plot the densities estimated from a mixture model for a copy number polymorphism |
posteriorSimulation | Run the MCMC simulation. |
posteriorSimulation-method | Run the MCMC simulation. |
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 |
sigma | Retrieve standard deviations of each component/batch mean. |
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. |
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 | Number of thinning intervals. |
thin-method | Number of thinning intervals. |
tracePlot | Create a trace plot of a parameter estimated by MCMC. |
tracePlot-method | Create a trace plot of a parameter estimated by MCMC. |
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 data, latent variable, and batch for given observation |