Constructs a CopyNumberModel from SB, SBP, MB, or MBP models

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. An automated approach for mapping mixture components to copy number states is provided by the mapComponents function. The mapping can also be done manually – see mapping<-. 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

Value

a MultiBatchCopyNumber instance

a MultiBatchCopyNumber instance

See Also

mapComponents copyNumber

Examples

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