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\name{inter-range-methods}
\alias{inter-range-methods}
\alias{isDisjoint}
\alias{isDisjoint,RangedSummarizedExperiment-method}
\alias{disjointBins}
\alias{disjointBins,RangedSummarizedExperiment-method}
\title{Inter range transformations of a RangedSummarizedExperiment object}
\description{
This man page documents the \emph{inter range transformations} that are
supported on \link{RangedSummarizedExperiment} objects.
}
\usage{
\S4method{isDisjoint}{RangedSummarizedExperiment}(x, ignore.strand=FALSE)
\S4method{disjointBins}{RangedSummarizedExperiment}(x, ignore.strand=FALSE)
}
\arguments{
\item{x}{
A \link{RangedSummarizedExperiment} object.
}
\item{ignore.strand}{
See \code{?\link[GenomicRanges]{isDisjoint}} in the
\pkg{GenomicRanges} package.
}
}
\details{
These transformations 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, any of the above functions performs the following
transformation on \link{RangedSummarizedExperiment} object \code{x}:
\preformatted{ f(rowRanges(x), ...)
}
where \code{f} is the name of the function and \code{...} any additional
arguments passed to it.
See \code{?\link[GenomicRanges]{isDisjoint}} in the \pkg{GenomicRanges}
package for the details of how these transformations operate on a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
}
\value{
See \code{?\link[GenomicRanges]{isDisjoint}} in the
\pkg{GenomicRanges} package.
}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item The \link[GenomicRanges]{isDisjoint} man page in the
\pkg{GenomicRanges} package where \emph{inter range transformations}
of a \link[GenomicRanges]{GenomicRanges} or
\link[GenomicRanges]{GRangesList} object 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)))
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, 99*start(rse0))
isDisjoint(rse0) # FALSE
isDisjoint(rse1) # TRUE
bins0 <- disjointBins(rse0)
bins0
stopifnot(identical(bins0, disjointBins(rowRanges(rse0))))
bins1 <- disjointBins(rse1)
bins1
stopifnot(all(bins1 == bins1[1]))
}
\keyword{methods}
\keyword{utilities}
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