callROH.PairedPSCBS

PairedPSCBS.callROH

callROH,PairedPSCBS-method

callROH.NonPairedPSCBS

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.

methods

internal

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome.  Both tumor-normal paired and tumor-only analyses are supported.

Henrik Bengtsson

PSCBS

Analysis of Parent-Specific DNA Copy Numbers

Pierre Neuvial

Venkatraman E. Seshan

Adam B. Olshen

Paul T. Spellman

Richard A. Olshen

Frank E Harrell Jr

callROH.PairedPSCBS function

<dl> <dt>...</dt>
<dd>Additional arguments passed to <code>testROH</code>().</dd> <dt>updateMeans</dt>
<dd>If <code><a href="/link/TRUE?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::TRUE">TRUE</a></code>, DH and (C1,C2) mean levels are set
 to <code><a href="/link/NA?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::NA">NA</a></code> for segments called ROH, otherwise not.</dd> <dt>force</dt>
<dd>If <code><a href="/link/FALSE?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::FALSE">FALSE</a></code>, and ROH calls already exits,
 then nothing is done, otherwise the calls are done.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

Calls segments that are in ROH — callROH.PairedPSCBS

<dl>

 <dt>...</dt>
<dd>Additional arguments passed to <code>testROH</code>().</dd>

 <dt>updateMeans</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, DH and (C1,C2) mean levels are set
 to <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code> for segments called ROH, otherwise not.</dd>

 <dt>force</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>FALSE</a></code>, and ROH calls already exits,
 then nothing is done, otherwise the calls are done.</dd>

 <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd>

</dl>

Calls segments that are in ROH

callROH.PairedPSCBS: Calls segments that are in ROH

Description

Usage

Value

Arguments

Author

See Also