DGEExact-class: differential expression of Digital Gene Expression data -...

Description List Components Methods Author(s) See Also

Description

A list-based S4 class for for storing results of a differential expression analysis for DGE data.

List Components

For objects of this class, rows correspond to genomic features and columns to statistics associated with the differential expression analysis. The genomic features are called genes, but in reality might correspond to transcripts, tags, exons etc.

Objects of this class contain the following list components:

table:

data frame containing columns for the log2-fold-change, logFC, the average log2-counts-per-million, logCPM, and the two-sided p-value PValue.

comparison:

vector giving the two experimental groups/conditions being compared.

genes:

a data frame containing information about each gene (can be NULL).

Methods

This class inherits directly from class list, so DGEExact 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 DGEExact object are defined by those of table, see dim.DGEExact or dimnames.DGEExact.

DGEExact objects can be subsetted, see subsetting.

DGEExact objects also have a show method so that printing produces a compact summary of their contents.

Author(s)

edgeR team. First created by Mark Robinson and Davis McCarthy

See Also

Other classes defined in edgeR are DGEList-class, DGEGLM-class, DGELRT-class, TopTags-class


edgeR documentation built on Nov. 17, 2017, 9:48 a.m.