estimateStandardDeviation.CBS

CBS.estimateStandardDeviation

estimateStandardDeviation,CBS-method

Estimates the whole-genome standard deviation of the signals.

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

estimateStandardDeviation.CBS function

<dl> <dt>chromosomes</dt>
<dd>An optional <code><a href="/link/vector?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::vector">vector</a></code> specifying the subset of
 chromosomes used for the estimate. If <code><a href="/link/NULL?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::NULL">NULL</a></code>, all chromosomes are used.</dd> <dt>method</dt>
<dd>A <code><a href="/link/character?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::character">character</a></code> string specifying the method used.</dd> <dt>estimator</dt>
<dd>A <code><a href="/link/character?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::character">character</a></code> string or a <code><a href="/link/function?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::function">function</a></code> specifying the
 internal estimator.</dd> <dt>na.rm</dt>
<dd>If <code><a href="/link/TRUE?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::TRUE">TRUE</a></code>, missing values are dropped, otherwise not.</dd> <dt>weights</dt>
<dd>An optional <code><a href="/link/double?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::double">double</a></code> <code><a href="/link/vector?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::vector">vector</a></code> of <code>nbrOfLoci()</code>
 non-negative weights.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Author

Estimates the whole-genome standard deviation of the signals — estimateStandardDeviation.CBS

<dl>

 <dt>chromosomes</dt>
<dd>An optional <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> specifying the subset of
 chromosomes used for the estimate. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, all chromosomes are used.</dd>

 <dt>method</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string specifying the method used.</dd>

 <dt>estimator</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string or a <code><a href='https://rdrr.io/r/base/function.html'>function</a></code> specifying the
 internal estimator.</dd>

 <dt>na.rm</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, missing values are dropped, otherwise not.</dd>

 <dt>weights</dt>
<dd>An optional <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of <code>nbrOfLoci()</code>
 non-negative weights.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

</dl>

Estimates the whole-genome standard deviation of the signals

estimateStandardDeviation.CBS: Estimates the whole-genome standard deviation of the signals

Description

Usage

Value

Arguments

Author

See Also