coverage-methods: Coverage of a RangedSummarizedExperiment object

Description Usage Arguments Details Value See Also Examples

Description

This man page documents the coverage method for RangedSummarizedExperiment objects.

Usage

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## 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

Examples

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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))))

SummarizedExperiment documentation built on Aug. 2, 2019, 2 a.m.