PSCBS (version 0.63.0)

callROH.PairedPSCBS: 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 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.

See Also

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