edgeR (version 3.14.0)

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.

Value

DGEList object

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.

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))
dim(d)
colnames(d)
d$samples