DGEList {edgeR} | R Documentation

## 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)

[Package edgeR version 3.36.0 Index]