SegList-class

print.SegList

show,SegList-method

[.SegList


A list based class for storing the results of a segmentation algorithm.
They are generally created by running one of the following functions
<code><a rd-options="" href="/link/runHomHMM?package=snapCGH&version=1.42.0" data-mini-rdoc="snapCGH::runHomHMM">runHomHMM</a></code>, <code><a rd-options="" href="/link/runGLAD?package=snapCGH&version=1.42.0" data-mini-rdoc="snapCGH::runGLAD">runGLAD</a></code> or <code><a rd-options="" href="/link/runDNAcopy?package=snapCGH&version=1.42.0" data-mini-rdoc="snapCGH::runDNAcopy">runDNAcopy</a></code>
on an <code><a rd-options="limma:malist" href="/link/MAList?package=snapCGH&version=1.42.0&to=limma%3Amalist" data-mini-rdoc="limma:malist::MAList">MAList</a> object</code>.


classes

data

Methods for segmenting, normalising and processing aCGH
data; including plotting functions for visualising raw and
segmented data for individual and multiple arrays.

John Marioni

snapCGH

Segmentation, normalisation and processing of aCGH data.

SegList-class function

Objects should contain the following list components:
<table><tr><td>
  <code>pred</code>:</td>
</tr><tr><td> Predicted value of the state.</td>
</tr><tr><td>
  <code>disp</code>:</td>
</tr><tr><td> Dispersion.</td>
</tr><tr><td>
  <code>obs</code>:</td>
</tr><tr><td> Observed value.</td>
</tr><tr><td>
  <code>state</code>:</td>
</tr><tr><td> Numeric value.</td>
</tr><tr><td>
  <code>nstates.hmm</code>: </td>
</tr><tr><td> The number of states per chromosome.  Each row represents a chromosome and each column is an array.</td>
</tr><tr><td>
  <code>genes</code>:</td>
</tr><tr><td> data.frame that contains the chromosome and position on the chromosome for each clone.  Used for plotting functions.</td>
</tr></table>
Optional:
<table><tr><td>
  <code>rpred</code>:</td>
</tr><tr><td> Smoothed value for the clone.</td>
</tr><tr><td>
  <code>prob</code>:</td>
</tr><tr><td> Probability of the clone being in the assigned state.</td>
</tr></table>

Slots/List Components

<code>SegLists</code> can be subsetted and combined.  They also return dimensions
so functions such as <code><a rd-options="base" href="/link/dim?package=snapCGH&version=1.42.0&to=base" data-mini-rdoc="base::dim">dim</a></code>, <code><a rd-options="base" href="/link/nrow?package=snapCGH&version=1.42.0&to=base" data-mini-rdoc="base::nrow">nrow</a></code> and
<code><a rd-options="base:nrow" href="/link/ncol?package=snapCGH&version=1.42.0&to=base%3Anrow" data-mini-rdoc="base:nrow::ncol">ncol</a></code> are also defined.  <code>SegList</code> inherits the
<code><a rd-options="methods" href="/link/show?package=snapCGH&version=1.42.0&to=methods" data-mini-rdoc="methods::show">show</a></code> method from the Limma class
<code><a rd-options="limma" href="/link/LargeDataObject?package=snapCGH&version=1.42.0&to=limma" data-mini-rdoc="limma::LargeDataObject">LargeDataObject</a></code>.  This means that the <code>SegList</code>
will print in a relatively compact way.

Methods

A list based class for storing the results of a segmentation algorithm.
They are generally created by running one of the following functions
<code><a href="runHomHMM" rd-options="">runHomHMM</a></code>, <code><a href="runGLAD" rd-options="">runGLAD</a></code> or <code><a href="runDNAcopy" rd-options="">runDNAcopy</a></code>
on an <code><a href="MAList" rd-options="limma:malist">MAList</a> object</code>.

SegList-class: Segmentation States - class

Description

Arguments

Slots/List Components

Methods