PSCBS (version 0.16.0)

callLOH.PairedPSCBS: Calls segments that are in LOH

Description

Calls segments that are in LOH, i.e. that have "zero" minor copy number.

Usage

## S3 method for class 'PairedPSCBS':
callLOH(fit, flavor=c("SmallC1", "LargeDH"), ..., minSize=1, xorCalls=TRUE, force=FALSE)

Arguments

flavor

A character string specifying which type of call to use.

...

Additional arguments passed to the caller.

minSize

An optional integer specifying the minimum number of data points in order to call a segments. If fewer data points, then the call is set to NA re

xorCalls

If TRUE, a region already called AB, will not be called LOH.

force

If FALSE, and allelic-balance calls already exits, then nothing is done, otherwise the calls are done.

Value

• Returns a PairedPSCBS object with LOH calls.

See Also

Internally, one of the following methods are used: *callLowC1ByC1(), *callExtremeAllelicImbalanceByDH().