callCopyNeutralByTCNofAB.PairedPSCBS

PairedPSCBS.callCopyNeutralByTCNofAB

callCopyNeutralByTCNofAB,PairedPSCBS-method

A PairedPSCBS fit object as returned by
    <code><a href="/link/segmentByPairedPSCBS?package=PSCBS&version=0.23.0&to=PSCBS" rd-options="PSCBS" data-mini-rdoc="PSCBS::segmentByPairedPSCBS">segmentByPairedPSCBS</a></code>.

A non-negative <code><a href="/link/double?package=PSCBS&version=0.23.0&to=base" rd-options="base" data-mini-rdoc="base::double">double</a></code> specifying the width of the
    "acceptance" region.

delta

A <code><a href="/link/double?package=PSCBS&version=0.23.0&to=base" rd-options="base" data-mini-rdoc="base::double">double</a></code> in [0,0.5] specifying the significance level
    of the confidence intervals used.

alpha

Additional arguments passed to
             <code><a href="/link/*calcStatsForCopyNeutralABs?package=PSCBS&version=0.23.0&to=PSCBS%3AcalcStatsForCopyNeutralABs.PairedPSCBS" rd-options="PSCBS:calcStatsForCopyNeutralABs.PairedPSCBS" data-mini-rdoc="PSCBS:calcStatsForCopyNeutralABs.PairedPSCBS::*calcStatsForCopyNeutralABs">*calcStatsForCopyNeutralABs</a>()</code>.

If <code><a href="/link/TRUE?package=PSCBS&version=0.23.0&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, an already called object is skipped, otherwise not.

force

See <code><a href="/link/Verbose?package=PSCBS&version=0.23.0&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Calls regions that are copy neutral from the total copy numbers (TCNs) of segments
 in allelic balance (AB).

methods

internal

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

callCopyNeutralByTCNofAB.PairedPSCBS: Calls regions that are copy neutral

Description

Usage

Arguments

Value