theta-method: Accessor for the theta parameter in the hierarchical mixture...

In scristia/CNPBayes: Bayesian mixture models for copy number polymorphisms

Description

The interpretation of theta depends on whether object is a MarginalModel or a BatchModel. For BatchModel, theta is a matrix of size B x K, where B is the number of batches and K is the number of components. Each column of the theta matrix can be interpreted as the batch means for a particular component. For objects of class MarginalModel (assumes no batch effect), theta is a vector of length K. Each element of theta can be interpreted as the mean for a component. See the following examples for accessing the current value of theta from a MixtureModel-derived object, and for plotting the chain of theta values.

Usage

theta(object)

theta(object) <- value

## S4 method for signature 'McmcChains'
theta(object)

Arguments

object	see showMethods(theta)
value	a numeric matrix of mixture component means: rows correspond to batches and columns correspond to the mixture component

Details

For a 4-component model at a CNV region with 8 batches, the theta matrix would have dimensions 8 x 4.

Value

A vector of length number of components or a matrix of size number of batches x number of components

Examples

## MarginalModel
## Not run: 
k(SingleBatchModelExample)
theta(SingleBatchModelExample)
plot.ts(theta(chains(SingleBatchModelExample)))
## BatchModel
k(MultiBatchModelExample)
length(unique(batch(MultiBatchModelExample)))
theta(MultiBatchModelExample)
## Plot means for batches in one component
plot.ts(theta(chains(MultiBatchModelExample))[, 1:3])

## End(Not run)

scristia/CNPBayes documentation built on Aug. 9, 2020, 7:31 p.m.