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CNPBayes

Bayesian mixture model for estimating copy number polymorphisms

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Version

Version

1.2.2

License

Artistic-2.0

Issues

5

Pull Requests

0

Stars

7

Forks

5

Maintainer

Jacob Carey

Last Published

February 15th, 2017

Functions in CNPBayes (1.2.2)

tau

Retrieve overall standard deviation.
y

Retrieve data.
Hyperparameters-class

An object to specify the hyperparameters of a model.
clusters

Accessor for extracting the kmeans clusters from a DensityModel instance
consensusCNP

Identify consensus start and stop coordinates of a copy number polymorphism
logPrior

Calculate log likelihood of prior for model
posterior_cases

Calculate posterior proportion of cases by component
posteriorSimulation

Run the MCMC simulation.
nu.0

Retrieve the shape parameter for the sigma.2 distribution.
tauc

Retrieve overall standard deviation at each iteration of the MCMC.
CNPBayes

Bayesian mixture models for copy number estimation
BatchModel-class

An object for running MCMC simulations.
batch

Retrieve batches from object.
downsample

Create tile labels for each observation
DensityModel

Constructor for DensityModel class
labelSwitching

Calculate proportion of relabeling instances
bic

Calculate BIC of a model
McmcParams-class

An object to specify MCMC options for a later simulation
m2.0

Retrieve the shape parameter for the tau2 distribution.
burnin

Number of burnin iterations.
map

Calculate the maximum a posteriori estimate of latent variable assignment.
tau2

Accessor for the tau2 parameter in the hierarchical mixture model
extract

extract data, latent variable, and batch for given observation
p

Retrieve mixture proportions.
simulateData

Create simulated data for testing.
HyperparametersBatch

Create an object of class 'HyperparametersBatch' for the batch mixture model
Hyperparameters

Create an object of class 'Hyperparameters'
pic

Retrieve mixture proportions at each iteration of the MCMC.
simulateBatchData

Create simulated batch data for testing.
z

Retrieve latent variable assignments.
nStarts

Number of MCMC chains.
plot

Plot the densities estimated from a mixture model for a copy number polymorphism
downSampleEachBatch

Create tile labels for each observation
k

Number of components.
log_lik

Retrieve log likelihood.
mapCnProbability

Probabiliistic copy number assigments.
marginalLikelihood

Compute the marginal likelihood of a converged model.
McmcParams

Create an object of class 'McmcParams' to specify iterations, burnin, etc.
sigmac

Retrieve standard deviation of each component/batch mean at each iteration of the MCMC.
sigma2

Retrieve the variances of each component and batch distribution
MarginalModelExample

This data is a simulated example of Marginal data
chromosome

Extract character vector of sequence names
eta.0

Retrieve the rate parameter for the tau2 distribution.
logBayesFactor

Compute the log bayes factor between models.
McmcChains-class

An object to hold estimated paraeters.
BatchModel

Create an object for running hierarchical MCMC simulations.
chains

Retrieve simulated chains from model object.
probz

Retrieve the probability of latent variable membership by observation.
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.
thin

Number of thinning intervals.
MarginalModel-class

The 'MarginalModel' class
hyperParams

Accessor for Hyperparameters object for a MixtureModel-derived object
tracePlot

Create a trace plot of a parameter estimated by MCMC.
oned

Retrieve data.
names,McmcChains-method

Retrieve the names of the parameters estimated in the MCMC chain.
qInverseTau2

Quantiles, shape, and rate of the prior for the inverse of tau2 (the precision)
sigma2.0

Retrieve the rate parameter for the sigma.2 distribution.
zFreq

Calculates a frequency table of latent variable assigments by observation.
muMean

Retrieve overall mean averaged across MCMC simulations.
MarginalModel

Create an object for running marginal MCMC simulations.
MixtureModel-class

An object for running MCMC simulations.
iter<-

Reset number of iterations.
collapseBatch

Estimate batch from a collection of chemistry plates or some other variable that captures the time in which the arrays were processed.
mu

Retrieve overall mean
sigma

Retrieve standard deviations of each component/batch mean.
theta

Accessor for the theta parameter in the hierarchical mixture model
saveBatch

Save se data
DensityModel-class

An object to store estimated mixture model densities
HyperparametersMarginal

Create an object of class 'HyperparametersMarginal' for the marginal mixture model
BatchModelExample

This data is a simulated example of Batch data
modes

Retrieve the modes from a model.
muc

Retrieve overall mean at each iteration of the MCMC.
tauMean

Retrieve overall standard deviation averaged across MCMC simulations.