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\name{intra-range-methods}
\alias{intra-range-methods}
\alias{shift}
\alias{shift,RangedSummarizedExperiment-method}
\alias{narrow}
\alias{narrow,RangedSummarizedExperiment-method}
\alias{resize}
\alias{resize,RangedSummarizedExperiment-method}
\alias{flank}
\alias{flank,RangedSummarizedExperiment-method}
\alias{promoters}
\alias{promoters,RangedSummarizedExperiment-method}
\alias{restrict}
\alias{restrict,RangedSummarizedExperiment-method}
\alias{trim,RangedSummarizedExperiment-method}
\title{Intra range transformations of a RangedSummarizedExperiment object}
\description{
This man page documents the \emph{intra range transformations} that are
supported on \link{RangedSummarizedExperiment} objects.
}
\usage{
\S4method{shift}{RangedSummarizedExperiment}(x, shift=0L, use.names=TRUE)
\S4method{narrow}{RangedSummarizedExperiment}(x, start=NA, end=NA, width=NA, use.names=TRUE)
\S4method{resize}{RangedSummarizedExperiment}(x, width, fix="start", use.names=TRUE,
ignore.strand=FALSE)
\S4method{flank}{RangedSummarizedExperiment}(x, width, start=TRUE, both=FALSE,
use.names=TRUE, ignore.strand=FALSE)
\S4method{promoters}{RangedSummarizedExperiment}(x, upstream=2000, downstream=200)
\S4method{restrict}{RangedSummarizedExperiment}(x, start=NA, end=NA, keep.all.ranges=FALSE,
use.names=TRUE)
\S4method{trim}{RangedSummarizedExperiment}(x, use.names=TRUE)
}
\arguments{
\item{x}{
A \link{RangedSummarizedExperiment} object.
}
\item{shift, use.names}{
See \code{?\link{shift}} in the \pkg{IRanges}
package.
}
\item{start, end, width, fix}{
See \code{?\link{shift}} in the \pkg{IRanges} package.
}
\item{ignore.strand, both}{
See \code{?\link{shift}} in the \pkg{IRanges} package.
}
\item{upstream, downstream}{
See \code{?\link{shift}} in the \pkg{IRanges} package.
}
\item{keep.all.ranges}{
See \code{?\link{shift}} in the \pkg{IRanges} 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{ rowRanges(x) <- f(rowRanges(x), ...)
}
where \code{f} is the name of the function and \code{...} any additional
arguments passed to it.
See \code{?\link{shift}} in the \pkg{IRanges}
package for the details of how these transformations operate on a
\link[GenomicRanges]{GenomicRanges} or \link[GenomicRanges]{GRangesList}
object.
}
\seealso{
\itemize{
\item \link{RangedSummarizedExperiment} objects.
\item The \link{shift} man page in the
\pkg{IRanges} package where \emph{intra 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, 1)
stopifnot(identical(
rowRanges(rse1),
shift(rowRanges(rse0), 1)
))
se2 <- narrow(rse0, start=10, end=-15)
stopifnot(identical(
rowRanges(se2),
narrow(rowRanges(rse0), start=10, end=-15)
))
se3 <- resize(rse0, width=75)
stopifnot(identical(
rowRanges(se3),
resize(rowRanges(rse0), width=75)
))
se4 <- flank(rse0, width=20)
stopifnot(identical(
rowRanges(se4),
flank(rowRanges(rse0), width=20)
))
se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
stopifnot(identical(
rowRanges(se5),
restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
))
}
\keyword{methods}
\keyword{utilities}
|
