callGNL.PairedPSCBS: Calls segments that are gained, copy neutral, or lost

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Calls segments that are gained, copy neutral, or lost

Description

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.

Usage

## S3 method for class 'PairedPSCBS'
callGNL(fit, flavor=c("TCN|AB"), ..., minSize=1, 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 regardless.
force	If FALSE, and copy-neutral calls already exits, then nothing is done, otherwise the calls are done.

Value

Returns a PairedPSCBS object with added calls.

Author(s)

Henrik Bengtsson

See Also

Internally, one of the following methods are used: callGNLByTCNofAB().

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.