CopyNumber-methods: Constructs a CopyNumberModel from SB, SBP, MB, or MBP models

In CNPBayes: Bayesian mixture models for copy number polymorphisms

Description

The mixture components do not necessarily reflect distinct copy number states, possibly due to skewed (non-Gaussian) log R ratios. While easy to fit skewed data with a finite mixture of Gaussians, additional steps are needed to assess whether the components correspond to distinct copy number states. This accessor copyNumber returns the copy number states – i.e., the result after mapping mixture components to copy number states.

Usage

CopyNumberModel(model, params = mapParams())

SingleBatchCopyNumber(model)

MultiBatchCopyNumber(model)

MultiBatchCopyNumberPooled(model)

## S4 method for signature 'SingleBatchModel'
CopyNumberModel(model, params = mapParams())

## S4 method for signature 'MultiBatchModel'
CopyNumberModel(model, params = mapParams())

## S4 method for signature 'MultiBatchPooled'
CopyNumberModel(model, params = mapParams())

mapCopyNumber(model, params = mapParams())

Arguments

model	a SB, SBP, MB, or MBP model
params	a list of parameters used for mapping mixture components to copy number states.

Value

a MultiBatchCopyNumber instance

a MultiBatchCopyNumber instance

See Also

copyNumber

Examples

sb <- SingleBatchModelExample
cn.model <- CopyNumberModel(sb, mapParams())

CNPBayes documentation built on May 6, 2019, 4:06 a.m.