DGEList: DGEList Constructor

In OliverVoogd/edgeR: Empirical Analysis of Digital Gene Expression Data in R

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.

See Also

DGEList-class

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)

OliverVoogd/edgeR documentation built on July 28, 2022, 10:13 p.m.