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\name{coverage-methods}
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\alias{coverage-methods}
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\alias{coverage,GenomicRanges-method}
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\alias{coverage,GRangesList-method}
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\alias{coverage,GappedAlignments-method}
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\alias{coverage,GappedAlignmentPairs-method}
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\title{Coverage of a GRanges, GRangesList, GappedAlignments, or
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GappedAlignmentPairs object}
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\code{\link[IRanges]{coverage}} methods for \link{GRanges},
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\link{GRangesList}, \link{GappedAlignments}, and \link{GappedAlignmentPairs}
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\S4method{coverage}{GenomicRanges}(x, shift=0L, width=NULL, weight=1L, ...)
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\S4method{coverage}{GappedAlignments}(x, shift=0L, width=NULL,
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weight=1L, drop.D.ranges=FALSE, ...)
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\S4method{coverage}{GappedAlignmentPairs}(x, shift=0L, width=NULL,
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weight=1L, drop.D.ranges=FALSE, ...)
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A \link{GRanges}, \link{GRangesList}, \link{GappedAlignments},
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or \link{GappedAlignmentPairs} object.
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\item{shift, width, weight, ...}{
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See \code{\link[IRanges]{coverage}} in the IRanges package for
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a description of these optional arguments.
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Whether the coverage calculation should ignore ranges corresponding
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to D (deletion) in the CIGAR string.
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Here is how optional arguments \code{shift}, \code{width} and
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\code{weight} are handled when \code{x} is a \link{GRanges} object:
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\item \code{shift}, \code{weight}: can be either a numeric vector
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(integers) or a list. If a list, then it should be named by the
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sequence levels in \code{x} (i.e. by the names of the underlying
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sequences), and its elements are passed into the \code{coverage}
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method for \link[IRanges]{IRanges} objects. If a numeric vector,
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then it is first recycled to the length of \code{x}, then turned
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into a list with \code{split(shift, as.factor(seqnames(x)))},
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and finally the elements of this list are passed into the
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\code{coverage} method for \link[IRanges]{IRanges} objects.
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Finally, if \code{x} is a \link{GRanges} object, then \code{weight}
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can also be a single string naming a metadata column to be used
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\item \code{width}: can be either \code{NULL} or a numeric vector.
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If a numeric vector, then it should be named by the sequence
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levels in \code{x}. If \code{NULL} (the default), then it is
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replaced with \code{seqlengths(x)}. Like for \code{shift} and
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\code{weight}, its elements are passed into the \code{coverage}
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method for \link[IRanges]{IRanges} objects (if the element is
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\code{NA} then \code{NULL} is passed instead).
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When \code{x} is a \link{GRangesList} object, \code{coverage(x, ...)}
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is equivalent to \code{coverage(unlist(x), ...)}.
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When \code{x} is a \link{GappedAlignments} or \link{GappedAlignmentPairs}
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object, \code{coverage(x, ...)} is equivalent to
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\code{coverage(as(x, "GRangesList"), ...)}.
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Returns a named \link[IRanges]{RleList} object with one element
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('integer' Rle) per underlying sequence in \code{x} representing how
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many times each position in the sequence is covered by the intervals in
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\author{P. Aboyoun and H. Pages}
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\item \code{\link[IRanges]{coverage}}.
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\item \link[IRanges]{RleList-class}.
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\item \link{GRanges-class}.
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\item \link{GRangesList-class}.
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\item \link{GappedAlignments-class}.
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\item \link{GappedAlignmentPairs-class}.
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## Coverage of a GRanges object:
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seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
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ranges=IRanges(1:10, end=10),
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strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
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seqlengths=c(chr1=11, chr2=12, chr3=13))
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pcvg <- coverage(gr[strand(gr) == "+"])
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mcvg <- coverage(gr[strand(gr) == "-"])
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scvg <- coverage(gr[strand(gr) == "*"])
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stopifnot(identical(pcvg + mcvg + scvg, cvg))
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## Coverage of a 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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grl <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
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stopifnot(identical(coverage(grl), coverage(unlist(grl))))
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## Coverage of a GappedAlignments or GappedAlignmentPairs object:
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library(Rsamtools) # because file ex1.bam is in this package
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ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
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galn <- readGappedAlignments(ex1_file)
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stopifnot(identical(coverage(galn), coverage(as(galn, "GRangesList"))))
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galp <- readGappedAlignmentPairs(ex1_file)
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stopifnot(identical(coverage(galp), coverage(as(galp, "GRangesList"))))
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man/coverage-methods.Rd
