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\name{coverage-methods}
\alias{coverage-methods}
\alias{coverage}
\alias{coverage,RangedSummarizedExperiment-method}
\title{Coverage of a RangedSummarizedExperiment object}
\description{
This man page documents the \code{coverage} method for
\link{RangedSummarizedExperiment} objects.
}
\usage{
\S4method{coverage}{RangedSummarizedExperiment}(x, shift=0L, width=NULL, weight=1L,
method=c("auto", "sort", "hash"))
}
\arguments{
\item{x}{
A \link{RangedSummarizedExperiment} object.
}
\item{shift, width, weight, method}{
See \code{?\link[GenomicRanges]{coverage}} in the \pkg{GenomicRanges}
package.
}
}
\details{
This method operates on the \code{rowRanges} component of the
\link{RangedSummarizedExperiment} object, which can be a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
More precisely, on \link{RangedSummarizedExperiment} object \code{x},
\code{coverage(x, ...)} is equivalent to \code{coverage(rowRanges(x), ...)}.
See \code{?\link[GenomicRanges]{coverage}} in the \pkg{GenomicRanges}
package for the details of how \code{coverage} operates on a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
}
\value{
See \code{?\link[GenomicRanges]{coverage}} in the \pkg{GenomicRanges}
package.
}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item The \link[GenomicRanges]{coverage} man page in the
\pkg{GenomicRanges} package where the \code{coverage} methods
for \link[GenomicRanges]{GenomicRanges} and
\link[GenomicRanges]{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))))
}
\keyword{methods}
\keyword{utilities}
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