DEDS-class

DEDS


  A simple list-based class to store DEDS results.<code>DEDS</code> objects
  are usually created  by functions <code><a rd-options="" href="/link/deds.pval?package=DEDS&version=1.46.0" data-mini-rdoc="DEDS::deds.pval">deds.pval</a></code>,
  <code><a rd-options="" href="/link/deds.stat?package=DEDS&version=1.46.0" data-mini-rdoc="DEDS::deds.stat">deds.stat</a></code> and <code><a rd-options="" href="/link/deds.stat.linkC?package=DEDS&version=1.46.0" data-mini-rdoc="DEDS::deds.stat.linkC">deds.stat.linkC</a></code>.


classes

data

This library contains functions that calculate various
statistics of differential expression for microarray data,
including t statistics, fold change, F statistics, SAM,
moderated t and F statistics and B statistics. It also
implements a new methodology called DEDS (Differential
Expression via Distance Summary), which selects differentially
expressed genes by integrating and summarizing a set of
statistics using a weighted distance approach.

Yuanyuan Xiao

Differential Expression via Distance Summary for Microarray Data

DEDS-class function

<code>DEDS</code> objects can be created by <code>new("DEDS",deds)</code> where
  <code>deds</code> is a list. This class contains no slots, but objects
  should contain the following list components:
  <table><tr><td>
    <code>E</code>: </td>
</tr><tr><td> A numeric vector of the most extreme point in the direction
      of differential expression. </td>
</tr><tr><td>
    <code>p</code>: </td>
</tr><tr><td> A numeric vector of q- or adjusted p-values.  </td>
</tr><tr><td>
    <code>geneOrder</code>:  </td>
</tr><tr><td> An integer vector giving the index of the top genes
      in terms of differential expression. </td>
</tr><tr><td>
    <code>stats</code>: </td>
</tr><tr><td> A matrix of p values or statistics. </td>
</tr></table>

Slots/List Components

This class inherits directly from class <code>list</code>, so any operation
  appropriate for lists will work on objects of this class. In addition,
  Other functions which operate on <code>DEDS</code> objects include
  <code><a rd-options="" href="/link/pairs?package=DEDS&version=1.46.0" data-mini-rdoc="DEDS::pairs">pairs</a></code> and <code><a rd-options="" href="/link/hist?package=DEDS&version=1.46.0" data-mini-rdoc="DEDS::hist">hist</a></code>.

Methods

A simple list-based class to store DEDS results.<code>DEDS</code> objects
  are usually created  by functions <code><a href="deds.pval" rd-options="">deds.pval</a></code>,
  <code><a href="deds.stat" rd-options="">deds.stat</a></code> and <code><a href="deds.stat.linkC" rd-options="">deds.stat.linkC</a></code>.

DEDS-class: DEDS Result List - class

Description

Arguments

Slots/List Components

Methods

See Also