DGELRT-class {edgeR} | R Documentation |
A simple list-based class for storing results of a GLM-based differential expression analysis for DGE data, with evidence for differential expression assessed using a likelihood ratio test.
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 tag.
coefficients.full
: matrix containing the coefficients
computed from fitting the full model (fit using glmFit
and a
given design matrix) to each gene/tag in the dataset.
coefficients.null
: matrix containing the coefficients
computed from fitting the null model to each gene/tag 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.
This class inherits directly from class list
so any operation appropriate for lists will work on objects of this class.
DGELRT
objects also have a show
method.
Davis McCarthy