CopyNumberModel {CNPBayes} | R Documentation |
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.
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())
model |
a SB, SBP, MB, or MBP model |
params |
a list of parameters used for mapping mixture components to copy number states. |
a MultiBatchCopyNumber
instance
a MultiBatchCopyNumber
instance
sb <- SingleBatchModelExample cn.model <- CopyNumberModel(sb, mapParams())