callGNL.PairedPSCBS

PairedPSCBS.callGNL

callGNL,PairedPSCBS-method

PairedPSCBS.callGainNeutralLoss

callGainNeutralLoss.PairedPSCBS

callGainNeutralLoss,PairedPSCBS-method

callGNLByTCNofAB

PairedPSCBS.callGNLByTCNofAB

callGNLByTCNofAB.PairedPSCBS

callGNLByTCNofAB,PairedPSCBS-method

callGNLByTCNofABv1

PairedPSCBS.callGNLByTCNofABv1

callGNLByTCNofABv1.PairedPSCBS

callGNLByTCNofABv1,PairedPSCBS-method

A <code><a href="/link/character?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::character">character</a></code> string specifying which type of
   call to use.

flavor

Additional arguments passed to the caller.

An optional <code><a href="/link/integer?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> specifying the minimum number
   of data points in order to call a segments.  If fewer data points,
   then the call is set to <code><a href="/link/NA?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::NA">NA</a></code> rega

minSize

If <code><a href="/link/FALSE?package=PSCBS&version=0.38.4&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::FALSE">FALSE</a></code>, and copy-neutral calls already exits,
   then nothing is done, otherwise the calls are done.

force

Calls segments that are gained, copy neutral, or lost, where copy neutral means having a total copy number
 that corresponds to the ploidy of the genome.

methods

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.

callGNL.PairedPSCBS: Calls segments that are gained, copy neutral, or lost

Description

Usage

Arguments

Value

See Also