AbstractCBS

A <code><a rd-options="base" href="/link/list?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::list">list</a></code> structure containing the segmentation results.

A <code><a rd-options="base" href="/link/character?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::character">character</a></code> string.

sampleName

Package: PSCBS 
Class AbstractCBS<code>list</code>
<code>~~|</code>
<code>~~+--</code><code>AbstractCBS</code>Directly known subclasses:
<a rd-options="PSCBS" href="/link/CBS?package=PSCBS&version=0.63.0&to=PSCBS" data-mini-rdoc="PSCBS::CBS">CBS</a>, <a rd-options="PSCBS" href="/link/NonPairedPSCBS?package=PSCBS&version=0.63.0&to=PSCBS" data-mini-rdoc="PSCBS::NonPairedPSCBS">NonPairedPSCBS</a>, <a rd-options="PSCBS" href="/link/PSCBS?package=PSCBS&version=0.63.0&to=PSCBS" data-mini-rdoc="PSCBS::PSCBS">PSCBS</a>, <a rd-options="PSCBS" href="/link/PairedPSCBS?package=PSCBS&version=0.63.0&to=PSCBS" data-mini-rdoc="PSCBS::PairedPSCBS">PairedPSCBS</a>
public abstract static class AbstractCBS
extends listAll CBS-style segmentation results extend this class, e.g.
 <code><a rd-options="" href="/link/CBS?package=PSCBS&version=0.63.0" data-mini-rdoc="PSCBS::CBS">CBS</a></code> and <code><a rd-options="" href="/link/PairedPSCBS?package=PSCBS&version=0.63.0" data-mini-rdoc="PSCBS::PairedPSCBS">PairedPSCBS</a></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

AbstractCBS function

Methods:<table><tr><td>
 </td>
<td> <code>adjustPloidyScale</code> </td>
<td> -</td>
</tr><tr><td>
 </td>
<td> <code>append</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>load</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>save</code> </td>
<td> -</td>
</tr><tr><td>
 </td>
<td> <code>writeWIG</code> </td>
<td> -</td>
</tr></table>Methods inherited from list:
all.equal, as.data.frame, attachLocally, callHooks, relist, within

Fields and Methods

A <code><a rd-options='base' href='list'>list</a></code> structure containing the segmentation results.

A <code><a rd-options='base' href='character'>character</a></code> string.

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

AbstractCBS: The AbstractCBS class

Description

Usage

Arguments

Fields and Methods