edgeR: DGEList – R documentation

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DGEList

DGEList Constructor

Description

Creates a DGEList object from a table of counts (rows=features, columns=samples), group indicator for each column, library size (optional) and a table of feature annotation (optional).

Usage

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

Arguments

`counts`	numeric matrix of read counts.
`lib.size`	numeric vector giving the total count (sequence depth) for each library.
`norm.factors`	numeric vector of normalization factors that modify the library sizes.
`samples`	data frame containing information for each sample.
`group`	vector or factor giving the experimental group/condition for each sample/library.
`genes`	data frame containing annotation information for each gene.
`remove.zeros`	logical, whether to remove rows that have 0 total count.

Details

To facilitate programming pipelines, NULL values can be input for lib.size, norm.factors, samples or group, in which case the default value is used as if the argument had been missing.

Value

a DGEList object

Author(s)

edgeR team. First created by Mark Robinson.

Examples

ngenes <- 1000
nsamples <- 4
Counts <- matrix(rnbinom(ngenes*nsamples,mu=5,size=2),ngenes,nsamples)
rownames(Counts) <- 1:ngenes
y <- DGEList(counts=Counts, group=rep(1:2,each=2))
dim(y)
colnames(y)
y$samples
y$genes <- data.frame(Symbol=paste0("Gene",1:ngenes))
show(y)

edgeR

Empirical Analysis of Digital Gene Expression Data in R

v3.32.1

GPL (>=2)

Authors

Yunshun Chen, Aaron TL Lun, Davis J McCarthy, Matthew E Ritchie, Belinda Phipson, Yifang Hu, Xiaobei Zhou, Mark D Robinson, Gordon K Smyth

Initial release

2021-01-14