DGELRT-class: Digital Gene Expression Likelihood Ratio Test data and...

In hiraksarkar/edgeR_fork: Empirical Analysis of Digital Gene Expression Data in R

Description

A list-based S4 class for storing results of a GLM-based 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 the log-concentration (i.e. expression level), the log-fold change in expression between the two groups/conditions and the exact p-value for differential expression, for each gene.

coefficients.full:

matrix containing the coefficients computed from fitting the full model (fit using glmFit and a given design matrix) to each gene in the dataset.

coefficients.null:

matrix containing the coefficients computed from fitting the null model to each gene in the dataset. The null model is the model to which the full model is compared, and is fit using glmFit and dropping selected column(s) (i.e. coefficient(s)) from the design matrix for the full model.

design:

design matrix for the full model from the likelihood ratio test.

...:

if the argument y to glmLRT (which produces the DGELRT object) was itself a DGEList object, then the DGELRT will contain all of the elements of y, except for the table of counts and the table of pseudocounts.

Methods

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

DGELRT objects can be subsetted, see subsetting.

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

Author(s)

edgeR team. First created by Davis McCarthy

See Also

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

hiraksarkar/edgeR_fork documentation built on Dec. 20, 2021, 3:52 p.m.