DGEList {edgeR}R Documentation

DGEList Constructor

Description

A function to create a DGEList object from a table of counts (rows=features, columns=samples), group indicator for each column, library size (optional) and a table of annotation (optional)

Usage

DGEList(counts = matrix(0, 0, 0), lib.size = NULL, norm.factors = NULL, group = rep.int(1,ncol(counts)), genes = NULL, remove.zeros = FALSE)

Arguments

counts

numeric matrix containing the read counts.

lib.size

numeric vector containing the total to normalize against for each sample (optional)

norm.factors

numeric vector containing normalization factors (optional, defaults to all 1)

group

vector giving the experimental group/condition for each sample/library

genes

data frame containing annotation information for the tags/transcripts/genes for which we have count data (optional).

remove.zeros

whether to remove rows that have 0 total count; default is FALSE so as to retain all information in the dataset

Details

If no lib.size argument is passed to the constructor, the column totals are used.

The optional genes argument supplies a data.frame of annotation for each row or feature.

Value

a DGEList object

Author(s)

Mark Robinson, Davis McCarthy, Gordon Smyth

See Also

DGEList-class

Examples

y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
d <- DGEList(counts=y, group=rep(1:2,each=2), lib.size=colSums(y))

[Package edgeR version 2.4.3 Index]