getBootstrapLocusSets.PairedPSCBS

PairedPSCBS.getBootstrapLocusSets

getBootstrapLocusSets,PairedPSCBS-method

getBootstrapLocusSets

Generates original and bootstrapped segment-specific index sets, which can be used to calculate various bootstrap summaries,
 e.g. segment mean levels.

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

getBootstrapLocusSets.PairedPSCBS function

<dl> <dt>B</dt>
<dd>A non-negative <code><a href="/link/integer?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::integer">integer</a></code> specifying the number of bootstrap samples.</dd> <dt>by</dt>
<dd>Should <code>betaTN</code> or <code>betaT</code> be used?</dd> <dt>seed</dt>
<dd>An (optional) <code><a href="/link/integer?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::integer">integer</a></code> specifying the random seed to be
 set before sampling indices. The random seed is set to its original
 state when exiting. If <code><a href="/link/NULL?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::NULL">NULL</a></code>, it is not set.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd> <dt>.validate</dt>
<dd>If <code><a href="/link/TRUE?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::TRUE">TRUE</a></code>, additional sanity checks are performed
 to validate the correctness. This is only needed for troubleshooting
 if it is suspected there is a bug.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Author

Generates original and bootstrapped segment-specific index sets — getBootstrapLocusSets.PairedPSCBS

<dl>

 <dt>B</dt>
<dd>A non-negative <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> specifying the number of bootstrap samples.</dd>

 <dt>by</dt>
<dd>Should <code>betaTN</code> or <code>betaT</code> be used?</dd>

 <dt>seed</dt>
<dd>An (optional) <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> specifying the random seed to be
 set before sampling indices. The random seed is set to its original
 state when exiting. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, it is not set.</dd>

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

 <dt>.validate</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, additional sanity checks are performed
 to validate the correctness. This is only needed for troubleshooting
 if it is suspected there is a bug.</dd>

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

</dl>

Generates original and bootstrapped segment-specific index sets

getBootstrapLocusSets.PairedPSCBS: Generates original and bootstrapped segment-specific index sets

Description

Usage

Value

Arguments

Author

See Also