getCounts {edgeR} | R Documentation

## Extract Specified Component of a DGEList Object

### Description

`getCounts(y)` returns the matrix of read counts `y$counts`.

`getOffset(y)` returns offsets for the log-linear predictor account for sequencing depth and possibly other normalization factors. Specifically it returns the matrix `y$offset` if it is non-null, otherwise it returns the log product of `lib.size` and `norm.factors` from `y$samples`.

`getDispersion(y)` returns the most complex dispersion estimates (common, trended or genewise) found in `y`.

### Usage

    getCounts(y)
    getOffset(y)
    getDispersion(y)

### Arguments

`y` | `DGEList` object containing (at least) the elements `counts` (table of raw counts), `group` (factor indicating group) and `lib.size` (numeric vector of library sizes)

### Value

`getCounts` returns the matrix of counts. `getOffset` returns a numeric matrix or vector. `getDispersion` returns vector of dispersion values.

### Author(s)

Mark Robinson, Davis McCarthy, Gordon Smyth

### See Also

`DGEList-class`

### Examples

    # generate raw counts from NB, create list object
    y <- matrix(rnbinom(20,size=5,mu=10),5,4)
    d <- DGEList(counts=y, group=c(1,1,2,2), lib.size=1001:1004)
    getCounts(d)
    getOffset(d)
    d <- estimateCommonDisp(d)
    getDispersion(d)

[Package edgeR version 3.24.3 Index]