callROH.PairedPSCBS: Calls segments that are in ROH

Description Usage Arguments Value Author(s) See Also

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

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## 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().


PSCBS documentation built on May 6, 2019, 1:05 a.m.