AbstractCBS

A <code><a href="/link/list?package=PSCBS&version=0.45.1&to=base" rd-options="base" data-mini-rdoc="base::list">list</a></code> structure containing the segmentation results.

A <code><a href="/link/character?package=PSCBS&version=0.45.1&to=base" rd-options="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 href="/link/CBS?package=PSCBS&version=0.45.1&to=PSCBS" rd-options="PSCBS" data-mini-rdoc="PSCBS::CBS">CBS</a>, <a href="/link/NonPairedPSCBS?package=PSCBS&version=0.45.1&to=PSCBS" rd-options="PSCBS" data-mini-rdoc="PSCBS::NonPairedPSCBS">NonPairedPSCBS</a>, <a href="/link/PSCBS?package=PSCBS&version=0.45.1&to=PSCBS" rd-options="PSCBS" data-mini-rdoc="PSCBS::PSCBS">PSCBS</a>, <a href="/link/PairedPSCBS?package=PSCBS&version=0.45.1&to=PSCBS" rd-options="PSCBS" data-mini-rdoc="PSCBS::PairedPSCBS">PairedPSCBS</a>public abstract static class AbstractCBSextends listAll CBS-style segmentation results extend this class, e.g.
 <code><a href="/link/CBS?package=PSCBS&version=0.45.1" rd-options="" data-mini-rdoc="PSCBS::CBS">CBS</a></code> and <code><a href="/link/PairedPSCBS?package=PSCBS&version=0.45.1" rd-options="" 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

AbstractCBS function

Methods:<tabular>rll</tabular>{
 	<code>adjustPloidyScale</code> 	-	<code>append</code> 	-	<code>extractCNs</code> 	-	<code>getChangePoints</code> 	-	<code>getChromosomes</code> 	-	<code>getLocusData</code> 	-	<code>getSegmentSizes</code> 	-	<code>getSegments</code> 	-	<code>load</code> 	-	<code>mergeThreeSegments</code> 	-	<code>nbrOfChangePoints</code> 	-	<code>nbrOfChromosomes</code> 	-	<code>nbrOfLoci</code> 	-	<code>nbrOfSegments</code> 	-	<code>ploidy</code> 	-	<code>ploidy&lt;-</code> 	-	<code>plotTracks</code> 	-	<code>sampleCNs</code> 	-	<code>save</code> 	-	<code>writeWIG</code> 	-}
 Methods inherited from list:all.equal, as.data.frame, attachLocally, callHooks, relist, within

AbstractCBS: The AbstractCBS class

Description

Usage

Arguments

Fields and Methods