plotDensity.GenomeInformation

GenomeInformation.plotDensity

plotDensity,GenomeInformation-method

Plots the density of SNPs for a given chromosome.

methods

internal

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system.  The only parameter that limits the number of chips that can be processed is the amount of available disk space.  The Aroma Framework has successfully been used in studies to process tens of thousands of arrays.  This package has actively been used since 2006.

Henrik Bengtsson

aroma.affymetrix

Analysis of Large Affymetrix Microarray Data Sets

James Bullard

Kasper Hansen

Pierre Neuvial

Elizabeth Purdom

Mark Robinson

Ken Simpson

plotDensity.GenomeInformation function

<dl> <dt>chromosome</dt>
<dd>The chromsome to be displayed.</dd> <dt>...</dt>
<dd>Additional arguments passed to <code>*getPositions()</code>.</dd> <dt>adjust</dt>
<dd>A bandwidth parameter for the density estimator.</dd> <dt>xlab</dt>
<dd>The label on the x-axis. If <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, a default will generated.</dd> <dt>main</dt>
<dd>The title of the plot. If <code><a href="/link/NULL?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::NULL">NULL</a></code>, a default will generated.</dd> <dt>annotate</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.affymetrix&version=3.2.2" data-mini-rdoc="aroma.affymetrix::TRUE">TRUE</a></code>, the plot is annotated with extra information.</dd></dl>

Arguments

Plots the density of SNPs for a given chromosome — plotDensity.GenomeInformation

<dl>

 <dt>chromosome</dt>
<dd>The chromsome to be displayed.</dd>

 <dt>...</dt>
<dd>Additional arguments passed to <code>*getPositions()</code>.</dd>

 <dt>adjust</dt>
<dd>A bandwidth parameter for the density estimator.</dd>

 <dt>xlab</dt>
<dd>The label on the x-axis. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, a default will generated.</dd>

 <dt>main</dt>
<dd>The title of the plot. If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, a default will generated.</dd>

 <dt>annotate</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, the plot is annotated with extra information.</dd>

</dl>

Plots the density of SNPs for a given chromosome

plotDensity.GenomeInformation: Plots the density of SNPs for a given chromosome

Description

Usage

Value

Arguments

See Also