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\name{findOverlaps-methods}
\alias{findOverlaps-methods}
\alias{findOverlaps}
\alias{findOverlaps,RangedSummarizedExperiment,Vector-method}
\alias{findOverlaps,Vector,RangedSummarizedExperiment-method}
\alias{findOverlaps,RangedSummarizedExperiment,RangedSummarizedExperiment-method}
\title{Finding overlapping ranges in RangedSummarizedExperiment objects}
\description{
This man page documents the \code{findOverlaps} methods for
\link{RangedSummarizedExperiment} objects.
\link{RangedSummarizedExperiment} objects also support
\code{countOverlaps}, \code{overlapsAny}, and \code{subsetByOverlaps}
thanks to the default methods defined in the \pkg{IRanges} package and
to the \code{findOverlaps} methods defined in this package and documented
below.
}
\usage{
\S4method{findOverlaps}{RangedSummarizedExperiment,Vector}(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
\S4method{findOverlaps}{Vector,RangedSummarizedExperiment}(query, subject,
maxgap=-1L, minoverlap=0L,
type=c("any", "start", "end", "within", "equal"),
select=c("all", "first", "last", "arbitrary"),
ignore.strand=FALSE)
}
\arguments{
\item{query, subject}{
One of these two arguments must be a \link{RangedSummarizedExperiment}
object.
}
\item{maxgap, minoverlap, type}{
See \code{?\link[GenomicRanges]{findOverlaps}} in the \pkg{GenomicRanges}
package.
}
\item{select, ignore.strand}{
See \code{?\link[GenomicRanges]{findOverlaps}} in the \pkg{GenomicRanges}
package.
}
}
\details{
These methods operate on the \code{rowRanges} component of the
\link{RangedSummarizedExperiment} object, which can be a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
More precisely, if any of the above functions is passed a
\link{RangedSummarizedExperiment} object thru the \code{query} and/or
\code{subject} argument, then it behaves as if \code{rowRanges(query)}
and/or \code{rowRanges(subject)} had been passed instead.
See \code{?\link[GenomicRanges]{findOverlaps}} in the \pkg{GenomicRanges}
package for the details of how \code{findOverlaps} and family operate on
\link[GenomicRanges]{GenomicRanges} and \link[GenomicRanges]{GRangesList}
objects.
}
\value{
See \code{?\link[GenomicRanges]{findOverlaps}} in the \pkg{GenomicRanges}
package.
}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item The \link[GenomicRanges]{findOverlaps} man page in the
\pkg{GenomicRanges} package where the \code{findOverlaps} family
of methods for \link[GenomicRanges]{GenomicRanges} and
\link[GenomicRanges]{GRangesList} objects is 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)))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
rse1 <- shift(rse0, 100)
hits <- findOverlaps(rse0, rse1)
hits
stopifnot(identical(hits, findOverlaps(rowRanges(rse0), rowRanges(rse1))))
stopifnot(identical(hits, findOverlaps(rse0, rowRanges(rse1))))
stopifnot(identical(hits, findOverlaps(rowRanges(rse0), rse1)))
}
\keyword{methods}
\keyword{utilities}
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