DGEList-class

A list-based S4 class for storing read counts and associated information from digital gene expression or sequencing technologies.

classes

The edge package implements methods for carrying out differential
    expression analyses of genome-wide gene expression studies. Significance testing
    using the optimal discovery procedure and generalized likelihood ratio tests
    (equivalent to F-tests and t-tests) are implemented for general study designs.
    Special functions are available to facilitate the analysis of common study
    designs, including time course experiments. Other packages such as snm, sva,
    and qvalue are integrated in edge to provide a wide range of tools for gene
    expression analysis.

John D Storey

edge

Extraction of Differential Gene Expression

DGEList-class function

This class inherits directly from class <code>list</code>, so <code>DGEList</code> objects can be manipulated as if they were ordinary lists.
However they can also be treated as if they were matrices for the purposes of subsetting.The dimensions, row names and column names of a <code>DGEList</code> object are defined by those of <code>counts</code>, see <code><a href="/link/dim.DGEList?package=edge&version=2.4.2" rd-options="" data-mini-rdoc="edge::dim.DGEList">dim.DGEList</a></code> or <code><a href="/link/dimnames.DGEList?package=edge&version=2.4.2" rd-options="" data-mini-rdoc="edge::dimnames.DGEList">dimnames.DGEList</a></code>.<code>DGEList</code> objects can be subsetted, see <code><a href="/link/subsetting?package=edge&version=2.4.2&to=edgeR%3Asubsetting" rd-options="edgeR:subsetting" data-mini-rdoc="edgeR:subsetting::subsetting">subsetting</a></code>.<code>DGEList</code> objects also have a <code>show</code> method so that printing produces a compact summary of their contents.

DGEList-class: Digital Gene Expression data - class

Description

Arguments

Methods

See Also