$,OPPARList-method

OPPARList-class

show,OPPARList-method

object

name


A S4 class for the output of OPPAR main function, opa.


The R implementation of mCOPA package published by Wang et al.
(2012). Oppar provides methods for Cancer Outlier profile Analysis. Although
initially developed to detect outlier genes in cancer studies, methods presented
in oppar can be used for outlier profile analysis in general. In addition,
tools are provided for gene set enrichment and pathway analysis.

Soroor Hediyeh zadeh

oppar

Outlier profile and pathway analysis in R

OPPARList-class function

<ul>
<li> <code>show</code>: A show method for objects of class OPPARList </li>
<li> <code>$</code>: A method to extract slots in <code>OPPARList</code>
</li>
</ul>

Methods (by generic)

 <dl>
<dt><code>profileMatrix</code></dt><dd>A matrix of 0, -1 and 1 representing outlier genes in samples</dd> <dt><code>upper.quantile</code></dt><dd>Numeric. The upper quantile cut-off for detection of outliers</dd> <dt><code>lower.quantile</code></dt><dd>Numeric. The lower quantile cut-off for detection of outliers</dd> <dt><code>group</code></dt><dd>A factor vector representing the group to which each sample belong</dd> <dt><code>.Data</code></dt><dd>matrix</dd> </dl>

OPPARList-class: A S4 class for the output of OPPAR main function, opa.

Description

Usage

Arguments

Value

Methods (by generic)

Slots