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\alias{intra-range-methods}
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\alias{shift,GenomicRanges-method}
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\alias{shift,GRangesList-method}
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\alias{narrow,GenomicRanges-method}
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\alias{narrow,GAlignments-method}
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\alias{narrow,GAlignmentsList-method}
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\alias{flank,GenomicRanges-method}
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\alias{flank,GRangesList-method}
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\alias{promoters,GenomicRanges-method}
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\alias{promoters,GRangesList-method}
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\alias{resize,GenomicRanges-method}
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\alias{Ops,GenomicRanges,numeric-method}
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\alias{restrict,GenomicRanges-method}
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\alias{restrict,GRangesList-method}
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\alias{trim,GenomicRanges-method}
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\title{Intra range transformations of a GenomicRanges object}
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\alias{Ops,GenomicRanges,numeric-method}
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\title{Intra range transformations of a GRanges or GRangesList object}
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See \code{?`\link[IRanges]{intra-range-methods}`} and
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\code{?`\link[IRanges]{inter-range-methods}`} in the IRanges package
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for a quick introduction to intra range and inter range transformations.
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This man page documents intra range transformations of a
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\link{GenomicRanges} object (i.e. of an object that belongs to the
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\link{GenomicRanges} class or one of its subclasses, this includes
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for example \link{GRanges} objects).
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for example \link{GRanges} objects), or a \link{GRangesList} object.
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See \code{?`\link[IRanges]{intra-range-methods}`} and
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\code{?`\link[IRanges]{inter-range-methods}`} in the \pkg{IRanges}
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package for a quick introduction to intra range and inter range
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Intra range methods for \link[GenomicAlignments]{GAlignments} and
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\link[GenomicAlignments]{GAlignmentsList} objects are defined and
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documented in the \pkg{GenomicAlignments} package.
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See \code{?`\link[GenomicRanges]{inter-range-methods}`} for
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inter range transformations of a GenomicRanges object.
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inter range transformations of a \link{GenomicRanges} or
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\link{GRangesList} object.
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\S4method{shift}{GenomicRanges}(x, shift=0L, use.names=TRUE)
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\S4method{shift}{GRangesList}(x, shift=0L, use.names=TRUE)
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\S4method{narrow}{GenomicRanges}(x, start=NA, end=NA, width=NA, use.names=TRUE)
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\S4method{narrow}{GAlignments}(x, start=NA, end=NA, width=NA, use.names=TRUE)
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\S4method{narrow}{GAlignmentsList}(x, start=NA, end=NA, width=NA, use.names=TRUE)
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\S4method{flank}{GenomicRanges}(x, width, start=TRUE, both=FALSE,
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use.names=TRUE, ignore.strand=FALSE)
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use.names=TRUE, ignore.strand=FALSE)
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\S4method{flank}{GRangesList}(x, width, start=TRUE, both=FALSE,
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use.names=TRUE, ignore.strand=FALSE)
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\S4method{promoters}{GenomicRanges}(x, upstream=2000, downstream=200, ...)
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\S4method{promoters}{GRangesList}(x, upstream=2000, downstream=200, ...)
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\S4method{resize}{GenomicRanges}(x, width, fix="start", use.names=TRUE,
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\S4method{restrict}{GenomicRanges}(x, start=NA, end=NA, keep.all.ranges=FALSE,
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\S4method{restrict}{GRangesList}(x, start=NA, end=NA, keep.all.ranges=FALSE,
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\S4method{trim}{GenomicRanges}(x, use.names=TRUE)
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\item{x}{A \link{GenomicRanges} object.}
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\item{x}{A \link{GenomicRanges} or \link{GRangesList} object.}
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\item{shift, use.names, start, end, width, both, fix, keep.all.ranges,
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upstream, downstream}{
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See \code{?`\link[IRanges]{intra-range-methods}`}.
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\link[IRanges]{Ranges} objects. See
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\code{?`\link[IRanges]{intra-range-methods}`} for the details.
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\item(){\code{narrow} on GenomicRanges objects behaves like the
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\code{narrow} method for \link[IRanges]{Ranges} objects. See
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\item(){\code{narrow} on a \link{GenomicRanges} object behaves
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like on a \link[IRanges]{Ranges} object. See
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\code{?`\link[IRanges]{intra-range-methods}`} for the details.
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When \code{x} is a \link{GAlignments} object, \code{narrow(x)}
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returns a new \link{GAlignments} object of the length of \code{x}
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describing the narrowed alignments. Unlike with \code{qnarrow}
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now the \code{start}/\code{end}/\code{width} arguments describe
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the narrowing on the reference side, not the query side.
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Like with \code{qnarrow}, they must be vectors of integers.
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NAs and negative values are accepted and "solved" according to the
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rules of the SEW (Start/End/Width) interface (see
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\code{?\link[IRanges]{solveUserSEW}} for the details).
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A major difference though is that it returns a \link{GenomicRanges}
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object instead of a \link[IRanges]{Ranges} object.
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The returned object is \emph{parallel} (i.e. same length and names)
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to the original object \code{x}.
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\item{}{\code{flank} returns an object of the same type and length
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as \code{x} containing intervals of width \code{width} that flank
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\item The \link{GenomicRanges} and \link{GRanges} classes.
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\item The \link[IRanges]{Ranges} class in the IRanges package.
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\item \link{GenomicRanges}, \link{GRanges}, and \link{GRangesList} objects.
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\item The \link[IRanges]{intra-range-methods} man page in the
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\pkg{IRanges} package.
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\item The \link[IRanges]{Ranges} class in the \pkg{IRanges} package.
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## ---------------------------------------------------------------------
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## A. ON A GRanges OBJECT
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## ---------------------------------------------------------------------
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seqnames=Rle(paste("chr", c(1, 2, 1, 3), sep=""), c(1, 3, 2, 4)),
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ranges=IRanges(1:10, width=10:1, names=letters[1:10]),
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gr <- GRanges("chr1", IRanges(rep(10, 3), width=6), c("+", "-", "*"))
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promoters(gr, 2, 2)
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## ---------------------------------------------------------------------
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## B. ON A GRangesList OBJECT
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## ---------------------------------------------------------------------
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gr1 <- GRanges("chr2", IRanges(3, 6))
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gr2 <- GRanges(c("chr1", "chr1"), IRanges(c(7,13), width=3),
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gr3 <- GRanges(c("chr1", "chr2"), IRanges(c(1, 4), c(3, 9)),
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grl <- GRangesList(gr1= gr1, gr2=gr2, gr3=gr3)
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flank(grl, width =20)
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restrict(grl, start=3)
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\keyword{utilities}
added
removed
man/intra-range-methods.Rd
