Coverage of a GRanges or GRangesList object

Description

coverage methods for GRanges and GRangesList objects.

NOTE: The coverage generic function and methods for Ranges and RangesList objects are defined and documented in the IRanges package. Methods for GAlignments and GAlignmentPairs objects are defined and documented in the GenomicAlignments package.

Usage

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## S4 method for signature 'GenomicRanges'
coverage(x, shift=0L, width=NULL, weight=1L,
            method=c("auto", "sort", "hash"))

## S4 method for signature 'GRangesList'
coverage(x, shift=0L, width=NULL, weight=1L,
            method=c("auto", "sort", "hash"))

Arguments

x

A GRanges or GRangesList object.

shift

A numeric vector or a list-like object. If numeric, it must be parallel to x (recycled if necessary). If a list-like object, it must have 1 list element per seqlevel in x, and its names must be exactly seqlevels(x).

Alternatively, shift can also be specified as a single string naming a metadata column in x (i.e. a column in mcols(x)) to be used as the shift vector.

See ?coverage in the IRanges package for more information about this argument.

width

Either NULL (the default), or an integer vector. If NULL, it is replaced with seqlengths(x). Otherwise, the vector must have the length and names of seqlengths(x) and contain NAs or non-negative integers.

See ?coverage in the IRanges package for more information about this argument.

weight

A numeric vector or a list-like object. If numeric, it must be parallel to x (recycled if necessary). If a list-like object, it must have 1 list element per seqlevel in x, and its names must be exactly seqlevels(x).

Alternatively, weight can also be specified as a single string naming a metadata column in x (i.e. a column in mcols(x)) to be used as the weight vector.

See ?coverage in the IRanges package for more information about this argument.

method

See ?coverage in the IRanges package for a description of this argument.

Details

When x is a GRangesList object, coverage(x, ...) is equivalent to coverage(unlist(x), ...).

Value

A named RleList object with one coverage vector per seqlevel in x.

Author(s)

H. Pag├Ęs and P. Aboyoun

See Also

  • coverage in the IRanges package.

  • coverage-methods in the GenomicAlignments package.

  • RleList objects in the IRanges package.

  • GRanges and GRangesList objects.

Examples

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## Coverage of a GRanges object:
gr <- GRanges(
        seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
        ranges=IRanges(1:10, end=10),
        strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
        seqlengths=c(chr1=11, chr2=12, chr3=13))
cvg <- coverage(gr)
pcvg <- coverage(gr[strand(gr) == "+"])
mcvg <- coverage(gr[strand(gr) == "-"])
scvg <- coverage(gr[strand(gr) == "*"])
stopifnot(identical(pcvg + mcvg + scvg, cvg))

## Coverage of a GRangesList object:
gr1 <- GRanges(seqnames="chr2",
               ranges=IRanges(3, 6),
               strand = "+")
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(7,13), width=3),
               strand=c("+", "-"))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
               ranges=IRanges(c(1, 4), c(3, 9)),
               strand=c("-", "-"))
grl <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
stopifnot(identical(coverage(grl), coverage(unlist(grl))))