Estimate confidence intervals of TCN and DH segment levels using bootstrap.

bootstrapTCNandDHByRegion.PairedPSCBS

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

bootstrapTCNandDHByRegion.PairedPSCBS function

Estimate confidence intervals of TCN and DH segment levels — bootstrapTCNandDHByRegion.PairedPSCBS

<dl>

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

 <dt>boot</dt>
<dd>Alternatively, to generating <code>B</code> bootstrap samples,
 this specifies a pre-generated set of bootstrap samples as
 returned by <code>bootstrapSegmentsAndChangepoints()</code>.</dd>

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

 <dt>probs</dt>
<dd>The default quantiles to be estimated.</dd>

 <dt>statsFcn</dt>
<dd>A (optional) <code><a href='https://rdrr.io/r/base/function.html'>function</a></code> that estimates confidence
 intervals given locus-level data.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, the <code><a href='https://rdrr.io/r/stats/quantile.html'>quantile</a></code> function is used.</dd>

 <dt>what</dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> specifying what to bootstrap.</dd>

 <dt>force</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, already existing estimates are ignored,
 otherwise not.</dd>

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

 <dt>.debug</dt>
<dd>(internal) If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, additional sanity checks are
 performed internally.</dd>

</dl>

Arguments

Author

Estimate confidence intervals of TCN and DH segment levels

bootstrapTCNandDHByRegion.PairedPSCBS: Estimate confidence intervals of TCN and DH segment levels

Description

Usage

Arguments

Value