AbstractCBS

Package: PSCBS 
Class AbstractCBS 
<code>list</code> 
<code>~~|</code> 
<code>~~+--</code><code>AbstractCBS</code> 
Directly known subclasses: 
CBS, NonPairedPSCBS, PSCBS, PairedPSCBS 
public abstract class AbstractCBS 
extends list 
All CBS-style segmentation results extend this class, e.g.
 <code>CBS</code> and <code>PairedPSCBS</code>.

classes

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

AbstractCBS function

<dl> <dt>fit</dt>
<dd>A <code><a href="/link/list?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::list">list</a></code> structure containing the segmentation results.</dd> <dt>sampleName</dt>
<dd>A <code><a href="/link/character?package=PSCBS&version=0.67.0" data-mini-rdoc="PSCBS::character">character</a></code> string.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Methods: <table class="table">
<tr><td></td><td><code>adjustPloidyScale</code></td><td>-</td></tr>
<tr><td></td><td><code>extractCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>getChangePoints</code></td><td>-</td></tr>
<tr><td></td><td><code>getChromosomes</code></td><td>-</td></tr>
<tr><td></td><td><code>getLocusData</code></td><td>-</td></tr>
<tr><td></td><td><code>getSegmentSizes</code></td><td>-</td></tr>
<tr><td></td><td><code>getSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>mergeThreeSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChangePoints</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChromosomes</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfLoci</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>normalizeTotalCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>ploidy</code></td><td>-</td></tr>
<tr><td></td><td><code>ploidy&lt;-</code></td><td>-</td></tr>
<tr><td></td><td><code>plotTracks</code></td><td>-</td></tr>
<tr><td></td><td><code>sampleCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>writeWIG</code></td><td>-</td></tr>
</table>Methods inherited from list: 
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.data.frame, attachLocally, callHooks, coerce,ANY,list-method, relist, type.convert, within

Fields and Methods

Author

Package: PSCBS 
Class AbstractCBS 
<code>list</code> 
<code>~~|</code> 
<code>~~+--</code><code>AbstractCBS</code> 
Directly known subclasses: 
CBS, NonPairedPSCBS, PSCBS, PairedPSCBS 
public abstract class AbstractCBS 
extends list 


All CBS-style segmentation results extend this class, e.g.
 <code>CBS</code> and <code>PairedPSCBS</code>.

The AbstractCBS class — AbstractCBS

<dl>

 <dt>fit</dt>
<dd>A <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> structure containing the segmentation results.</dd>

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

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

</dl>

Methods: <table class='table'>
<tr><td></td><td><code>adjustPloidyScale</code></td><td>-</td></tr>
<tr><td></td><td><code>extractCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>getChangePoints</code></td><td>-</td></tr>
<tr><td></td><td><code>getChromosomes</code></td><td>-</td></tr>
<tr><td></td><td><code>getLocusData</code></td><td>-</td></tr>
<tr><td></td><td><code>getSegmentSizes</code></td><td>-</td></tr>
<tr><td></td><td><code>getSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>mergeThreeSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChangePoints</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfChromosomes</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfLoci</code></td><td>-</td></tr>
<tr><td></td><td><code>nbrOfSegments</code></td><td>-</td></tr>
<tr><td></td><td><code>normalizeTotalCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>ploidy</code></td><td>-</td></tr>
<tr><td></td><td><code>ploidy&lt;-</code></td><td>-</td></tr>
<tr><td></td><td><code>plotTracks</code></td><td>-</td></tr>
<tr><td></td><td><code>sampleCNs</code></td><td>-</td></tr>
<tr><td></td><td><code>writeWIG</code></td><td>-</td></tr>
</table>



Methods inherited from list: 
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.data.frame, attachLocally, callHooks, coerce,ANY,list-method, relist, type.convert, within

	`adjustPloidyScale`	-
	`extractCNs`	-
	`getChangePoints`	-
	`getChromosomes`	-
	`getLocusData`	-
	`getSegmentSizes`	-
	`getSegments`	-
	`mergeThreeSegments`	-
	`nbrOfChangePoints`	-
	`nbrOfChromosomes`	-
	`nbrOfLoci`	-
	`nbrOfSegments`	-
	`normalizeTotalCNs`	-
	`ploidy`	-
	`ploidy<-`	-
	`plotTracks`	-
	`sampleCNs`	-
	`writeWIG`	-

AbstractCBS: The AbstractCBS class

Description

Usage

Arguments

Fields and Methods

Author