rCGH-class

Class <code>"<links4class>rCGH</links4class>"</code> is a superclass living on top of
<code>"<links4class>rCGH-Agilent</links4class>"</code>, <code>"<links4class>rCGH-SNP6</links4class>"</code>, 
<code>"<links4class>rCGH-cytoScan</links4class>"</code>, and <code>"<links4class>rCGH-generic</links4class>"</code>.
These objects inherit most of the properties of the superclass, and allow
specific parameterizations used during the analysis process.Objects are created by platform-specific <code>read</code> functions:
<code>"<a href="/link/readAgilent?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::readAgilent">readAgilent</a>"</code>, <code>"<a href="/link/readAffySNP6?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::readAffySNP6">readAffySNP6</a>"</code>,
and <code>"<a href="/link/readAffyCytoScan?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::readAffyCytoScan">readAffyCytoScan</a>"</code>,
each corresponding to their matched file format.A supplementary <code>"<a href="/link/readGeneric?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::readGeneric">readGeneric</a>"</code> allows the user to create a 
<code>"<links4class>rCGH</links4class>"</code> object from custom arrays.
Slots described below are used to store sample information and analysis
parameters, as well as segmentation results. All are accessible through specific
<code>"<a href="/link/Accessors?package=rCGH&version=1.2.2" rd-options="" data-mini-rdoc="rCGH::Accessors">Accessors</a>"</code> functions.

classes

A comprehensive pipeline for analyzing and interactively 
    visualizing genomic profiles generated through commercial or custom aCGH
    arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction
    files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD
    probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or
    Affymetrix Power Tools. rCGH also supports custom arrays, provided data is
    in a suitable format. This package takes over all the steps required for
    individual genomic profiles analysis, from reading files to segmenting
    and annotating genes. This package provides several visualization functions
    (static or interactive) which facilitate individual profiles interpretation.
    Input files can be in compressed format, e.g. .bz2 or .gz.

Frederic Commo

rCGH

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

rCGH-class function

Objects can be created by calls of the form <code>new("rCGH", ...)</code>.Slots content are updated at each different analysis step, and are accessible
through specific <code>get</code> functions.

Objects from the Class

Class <code>"<linkS4class>rCGH</linkS4class>"</code> is a superclass living on top of
<code>"<linkS4class>rCGH-Agilent</linkS4class>"</code>, <code>"<linkS4class>rCGH-SNP6</linkS4class>"</code>, 
<code>"<linkS4class>rCGH-cytoScan</linkS4class>"</code>, and <code>"<linkS4class>rCGH-generic</linkS4class>"</code>.
These objects inherit most of the properties of the superclass, and allow
specific parameterizations used during the analysis process.Objects are created by platform-specific <code>read</code> functions:
<code>"<a href="readAgilent" rd-options="">readAgilent</a>"</code>, <code>"<a href="readAffySNP6" rd-options="">readAffySNP6</a>"</code>,
and <code>"<a href="readAffyCytoScan" rd-options="">readAffyCytoScan</a>"</code>,
each corresponding to their matched file format.A supplementary <code>"<a href="readGeneric" rd-options="">readGeneric</a>"</code> allows the user to create a 
<code>"<linkS4class>rCGH</linkS4class>"</code> object from custom arrays.
Slots described below are used to store sample information and analysis
parameters, as well as segmentation results. All are accessible through specific
<code>"<a href="Accessors" rd-options="">Accessors</a>"</code> functions.

rCGH-class: Class `"rCGH"`

Description

Arguments

Objects from the Class

See Also

Examples