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\alias{union,GRanges,GRanges-method}
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\alias{intersect,GRanges,GRanges-method}
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\alias{setdiff,GRanges,GRanges-method}
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\alias{punion,GRanges,GRanges-method}
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\alias{punion,GRanges,GRangesList-method}
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\alias{punion,GRangesList,GRanges-method}
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\alias{pintersect,GRanges,GRanges-method}
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\alias{pintersect,GRanges,GRangesList-method}
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\alias{pintersect,GRangesList,GRanges-method}
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\alias{pintersect,GRangesList,GRangesList-method}
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\alias{pintersect,GappedAlignments,GRanges-method}
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\alias{pintersect,GRanges,GappedAlignments-method}
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\alias{psetdiff,GRanges,GRanges-method}
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\alias{psetdiff,GRanges,GRangesList-method}
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\alias{psetdiff,GRangesList,GRangesList-method}
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\alias{pgap,GRanges,GRanges-method}
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\title{Set operations on GRanges/GRangesList/GappedAlignments objects}
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Performs set operations on GRanges/GRangesList/GappedAlignments objects.
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\S4method{union}{GRanges,GRanges}(x, y, ignore.strand=FALSE, ...)
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\S4method{intersect}{GRanges,GRanges}(x, y, ignore.strand=FALSE, ...)
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\S4method{setdiff}{GRanges,GRanges}(x, y, ignore.strand=FALSE, ...)
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## Parallel set operations
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\S4method{punion}{GRanges,GRanges}(x, y, fill.gap=FALSE, ignore.strand=FALSE, ...)
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\S4method{pintersect}{GRanges,GRanges}(x, y, resolve.empty=c("none", "max.start", "start.x"), ignore.strand=FALSE, ...)
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\S4method{pintersect}{GappedAlignments,GRanges}(x, y, ...)
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\S4method{psetdiff}{GRanges,GRanges}(x, y, ignore.strand=FALSE, ...)
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For \code{union}, \code{intersect}, \code{setdiff}, \code{pgap}:
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\code{x} and \code{y} must both be \link{GRanges} objects.
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For \code{punion}: one of \code{x} or \code{y} must be a \link{GRanges}
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object, the other one can be a \link{GRanges} or \link{GRangesList} object.
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For \code{pintersect}: one of \code{x} or \code{y} must be a \link{GRanges}
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object, the other one can be a \link{GRanges}, \link{GRangesList} or
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\link{GappedAlignments} object.
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For \code{psetdiff}: \code{x} and \code{y} can be any combination of
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\link{GRanges} and/or \link{GRangesList} objects, with the exception
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that if \code{x} is a \link{GRangesList} object then \code{y} must be
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a \link{GRangesList} too.
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In addition, for the "parallel" operations, \code{x} and \code{y} must
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be of equal length (i.e. \code{length(x) == length(y)}).
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Logical indicating whether or not to force a union by using the rule
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\code{start = min(start(x), start(y)), end = max(end(x), end(y))}.
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One of \code{"none"}, \code{"max.start"}, or \code{"start.x"} denoting
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how to handle ambiguous empty ranges formed by intersections.
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\code{"none"} - throw an error if an ambiguous empty range is formed,
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\code{"max.start"} - associate the maximum start value with any
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ambiguous empty range, and \code{"start.x"} - associate the start value
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of \code{x} with any ambiguous empty range. (See
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\code{\link[IRanges]{pintersect}} for the definition of an ambiguous
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For set operations: If set to TRUE, then the strand of \code{x} and
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\code{y} is set to \code{"*"} prior to any computation.
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For parallel set operations: If set to TRUE, the strand information is
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ignored in the computation and the result has the strand information of
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Further arguments to be passed to or from other methods.
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The \code{pintersect} methods involving \link{GRanges}, \link{GRangesList}
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and/or \link{GappedAlignments} objects use the triplet (sequence name, range,
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strand) to determine the element by element intersection of features,
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where a strand value of \code{"*"} is treated as occurring on both the
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\code{"+"} and \code{"-"} strand.
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The \code{psetdiff} methods involving \link{GRanges} and/or
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\link{GRangesList} objects use the triplet (sequence name, range,
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strand) to determine the element by element set difference of features,
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where a strand value of \code{"*"} is treated as occurring on both the
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\code{"+"} and \code{"-"} strand.
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For \code{union}, \code{intersect}, \code{setdiff}, and \code{pgap}: a
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For \code{punion} and \code{pintersect}: when \code{x} or \code{y} is
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not a \link{GRanges} object, an object of the same class as this
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non-\link{GRanges} object. Otherwise, a \link{GRanges} object.
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For \code{psetdiff}: either a \link{GRanges} object when both \code{x}
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and \code{y} are \link{GRanges} objects, or a \link{GRangesList} object
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when \code{y} is a \link{GRangesList} object.
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\link[IRanges]{setops-methods},
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\link{GRanges-class},
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\link{GRangesList-class},
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\link{GappedAlignments-class},
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\link{findOverlaps-methods}
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## ---------------------------------------------------------------------
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## ---------------------------------------------------------------------
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x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
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y <- GRanges("chr1", IRanges(5, 10), strand="-")
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union(x, y, ignore.strand=TRUE)
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intersect(x, y, ignore.strand=TRUE)
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setdiff(x, y, ignore.strand=TRUE)
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## ---------------------------------------------------------------------
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## B. PARALLEL SET OPERATIONS
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## ---------------------------------------------------------------------
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punion(x, shift(x, 7)) # will fail
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punion(x, shift(x, 7), fill.gap=TRUE)
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pintersect(x, shift(x, 6))
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pintersect(x, shift(x, 7)) # will fail
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pintersect(x, shift(x, 7), resolve.empty="max.start")
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psetdiff(x, shift(x, 7))
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## ---------------------------------------------------------------------
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## ---------------------------------------------------------------------
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gr <- GRanges(seqnames=c("chr2", "chr1", "chr1"),
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ranges=IRanges(1:3, width = 12),
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strand=Rle(strand(c("-", "*", "-"))))
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## GRangesList object
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gr1 <- GRanges(seqnames="chr2",
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ranges=IRanges(3, 6))
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gr2 <- GRanges(seqnames=c("chr1", "chr1"),
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ranges=IRanges(c(7,13), width = 3),
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gr3 <- GRanges(seqnames=c("chr1", "chr2"),
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ranges=IRanges(c(1, 4), c(3, 9)),
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grlist <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
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## Parallel intersection of a GRanges and a GRangesList object
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pintersect(gr, grlist)
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pintersect(grlist, gr)
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## Parallel intersection of a GappedAlignments and a GRanges object
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library(Rsamtools) # because file ex1.bam is in this package
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galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
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galn <- readGappedAlignments(galn_file)
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pintersect(galn, shift(as(galn, "GRanges"), 6L))
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## Parallel set difference of a GRanges and a GRangesList object
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## Parallel set difference of two GRangesList objects
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psetdiff(grlist, shift(grlist, 3))
added
removed
man/setops-methods.Rd
