plotTracks.PairedPSCBS

PairedPSCBS.plotTracks

plotTracks,PairedPSCBS-method

PairedPSCBS.plotTracks1

plotTracks1.PairedPSCBS

plotTracks1,PairedPSCBS-method

PairedPSCBS.plotTracks2

plotTracks2.PairedPSCBS

plotTracks2,PairedPSCBS-method

PairedPSCBS.plotTracksManyChromosomes

plotTracksManyChromosomes.PairedPSCBS

plotTracksManyChromosomes,PairedPSCBS-method

plot

A result object returned by <code><a href="/link/segmentByPairedPSCBS?package=PSCBS&version=0.38.4" rd-options="" data-mini-rdoc="PSCBS::segmentByPairedPSCBS">segmentByPairedPSCBS</a></code>().

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> <code><a href="/link/vector?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> specifying what types of tracks to plot.

tracks

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> <code><a href="/link/vector?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> specifying which of the tracks should
    have scatter plot.

scatter

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> <code><a href="/link/vector?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of regular expression identifying
    call labels to be highlighted in the panels.

calls

If <code><a href="/link/TRUE?package=PSCBS&version=0.38.4&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, changepoints are drawn as vertical lines.

changepoints

If <code><a href="/link/TRUE?package=PSCBS&version=0.38.4&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, horizontal lines are displayed.

grid

A <code><a href="/link/numeric?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.38.4&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> in [0,1] specifying the quantiles
     of the confidence bands to be drawn, if any.

quantiles

xlim

Clim

The range of allele B fractions (BAFs) and
    decrease of heterozygosity (DHs).

Blim

The scale factor used for genomic positions.

xScale

If <code><a href="/link/TRUE?package=PSCBS&version=0.38.4&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, the panels plotted are added to the existing plot,
    otherwise a new plot is created.

If <code><a href="/link/TRUE?package=PSCBS&version=0.38.4&to=base%3Alogical" rd-options="base:logical" data-mini-rdoc="base:logical::TRUE">TRUE</a></code>, then subplots are automatically setup.

subplots

See <code><a href="/link/Verbose?package=PSCBS&version=0.38.4&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Plots parental specific copy numbers along the genome for one or more chromosomes.
 It is possible to specify what type of tracks to plot.
 Each type of track is plotted in its own panel.

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.

plotTracks.PairedPSCBS: Plots parental specific copy numbers along the genome

Description

Usage

Arguments

Value