callROH.PairedPSCBS: Calls segments that are in ROH

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

Calls segments that are in ROH

Description

Calls segments that are in ROH, i.e. that have no (true) heterozygous genotypes. Run of homozygosity (ROH) is a property of the normal (germline) sample.

Usage

## S3 method for class 'PairedPSCBS'
callROH(fit, ..., updateMeans=TRUE, force=FALSE, verbose=FALSE)

Arguments

...	Additional arguments passed to testROH().
updateMeans	If TRUE, DH and (C1,C2) mean levels are set to NA for segments called ROH, otherwise not.
force	If FALSE, and ROH calls already exits, then nothing is done, otherwise the calls are done.
verbose	See Verbose.

Value

Returns a PairedPSCBS object with ROH calls.

Author(s)

Pierre Neuvial, Henrik Bengtsson

See Also

Internally, testROH() is used. To call allelic balance (AB) see *callAB(). To call loss of heterozygosity (LOH) see *callLOH().

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