coverage-methods: Coverage of a RangedSummarizedExperiment object
In LiNk-NY/SummarizedExperiment: SummarizedExperiment container

Description Usage Arguments Details Value See Also Examples

This man page documents the coverage method for RangedSummarizedExperiment objects.

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

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

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.

See ?coverage in the GenomicRanges package.

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

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))))