coverage-methods {SummarizedExperiment} | R Documentation

## Coverage of a RangedSummarizedExperiment object

### Description

This man page documents the `coverage` method for RangedSummarizedExperiment objects.

### Usage

    ## S4 method for signature 'RangedSummarizedExperiment'
    coverage(x, shift=0L, width=NULL, weight=1L,
                method=c("auto", "sort", "hash"))

### Arguments

`x` | A RangedSummarizedExperiment object.
`shift, width, weight, method` | See `?coverage` in the GenomicRanges package.

### Details

This method operates on the `rowRanges` component of the RangedSummarizedExperiment object, which can be a GenomicRanges or GRangesList object.

More precisely, on RangedSummarizedExperiment object `x`, `coverage(x, ...)` is equivalent to `coverage(rowRanges(x), ...)`.

See `?coverage` in the GenomicRanges package for the details of how `coverage` operates on a GenomicRanges or GRangesList object.

### Value

See `?coverage` in the GenomicRanges package.

### See Also

- RangedSummarizedExperiment objects.

- The coverage man page in the GenomicRanges package where the `coverage` methods for GenomicRanges and GRangesList objects are documented.

### Examples

    nrows <- 20; ncols <- 6
    counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
    rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
                         IRanges(sample(1000L, 20), width=100),
                         strand=Rle(c("+", "-"), c(12, 8)),
                         seqlengths=c(chr1=1800, chr2=1300))
    colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                         row.names=LETTERS[1:6])
    rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
                                rowRanges=rowRanges, colData=colData)

    cvg <- coverage(rse)
    cvg
    stopifnot(identical(cvg, coverage(rowRanges(rse))))

[Package SummarizedExperiment version 1.10.1 Index]