PairedPSCBS

A <code><a href="/link/list?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::list">list</a></code> structure containing the Paired PSCBS results.

Package: PSCBS Class PairedPSCBS<code>list</code><code>~~|</code><code>~~+--</code><code>PairedPSCBS</code>Directly known subclasses:public class PairedPSCBSextends listA PairedPSCBS is an object containing the results from the
 Paired PSCBS method.

classes

Segments allele-specific DNA copy number data to detect
        regions with abnormal copy number within each parental
        chromosome

Henrik Bengtsson

PSCBS

Analysis of Parent-Specific DNA Copy Numbers

PairedPSCBS function

Methods:<tabular>rll</tabular>{
 	<code><a href="/link/as.data.frame?package=PSCBS&version=0.12.2&to=PSCBS%3Aas.data.frame.PairedPSCBS" rd-options="PSCBS:as.data.frame.PairedPSCBS" data-mini-rdoc="PSCBS:as.data.frame.PairedPSCBS::as.data.frame">as.data.frame</a></code> 	Gets the table of segments.	<code><a href="/link/callAB?package=PSCBS&version=0.12.2&to=PSCBS%3AcallAB.PairedPSCBS" rd-options="PSCBS:callAB.PairedPSCBS" data-mini-rdoc="PSCBS:callAB.PairedPSCBS::callAB">callAB</a></code> 	Calls segments that are in allelic balance.	<code><a href="/link/callLOH?package=PSCBS&version=0.12.2&to=PSCBS%3AcallLOH.PairedPSCBS" rd-options="PSCBS:callLOH.PairedPSCBS" data-mini-rdoc="PSCBS:callLOH.PairedPSCBS::callLOH">callLOH</a></code> 	Calls segments that are in LOH.	<code>callSegments</code> 	-	<code><a href="/link/estimateDeltaAB?package=PSCBS&version=0.12.2&to=PSCBS%3AestimateDeltaAB.PairedPSCBS" rd-options="PSCBS:estimateDeltaAB.PairedPSCBS" data-mini-rdoc="PSCBS:estimateDeltaAB.PairedPSCBS::estimateDeltaAB">estimateDeltaAB</a></code> 	Estimate a threshold for calling allelic balance from DH.	<code><a href="/link/estimateDeltaLOH?package=PSCBS&version=0.12.2&to=PSCBS%3AestimateDeltaLOH.PairedPSCBS" rd-options="PSCBS:estimateDeltaLOH.PairedPSCBS" data-mini-rdoc="PSCBS:estimateDeltaLOH.PairedPSCBS::estimateDeltaLOH">estimateDeltaLOH</a></code> 	Estimate a threshold for calling LOH from DH.	<code><a href="/link/estimateKappa?package=PSCBS&version=0.12.2&to=PSCBS%3AestimateKappa.PairedPSCBS" rd-options="PSCBS:estimateKappa.PairedPSCBS" data-mini-rdoc="PSCBS:estimateKappa.PairedPSCBS::estimateKappa">estimateKappa</a></code> 	Estimate global background in segmented copy numbers.	<code>extractC1C2</code> 	-	<code>extractTCNAndDHs</code> 	-	<code><a href="/link/plotTracks?package=PSCBS&version=0.12.2&to=PSCBS%3AplotTracks.PairedPSCBS" rd-options="PSCBS:plotTracks.PairedPSCBS" data-mini-rdoc="PSCBS:plotTracks.PairedPSCBS::plotTracks">plotTracks</a></code> 	Plots parental specific copy numbers along the genome.	<code>plotTracks2</code> 	-	<code>plotTracksManyChromosomes</code> 	-}


 Methods inherited from list:all.equal, as.data.frame, attachLocally, callHooks, relist, within

PairedPSCBS: The PairedPSCBS class

Description

Usage

Arguments

Fields and Methods

See Also