Calls segments that are gained, copy neutral, or lost, where copy neutral means having a total copy number that corresponds to the ploidy of the genome.
# S3 method for PairedPSCBS
callGNL(fit, flavor=c("TCN|AB"), ..., minSize=1, force=FALSE)Returns a PairedPSCBS object with added calls.
A character string specifying which type of
call to use.
Additional arguments passed to the caller.
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 regardless.
If FALSE, and copy-neutral calls already exits,
then nothing is done, otherwise the calls are done.
Henrik Bengtsson
Internally, one of the following methods are used:
callGNLByTCNofAB().