edge (version 2.4.2)

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

• a 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