R: Coverage of a GRanges, GRangesList, GAlignments, or...

coverage-methods {GenomicRanges}

R Documentation

Coverage of a GRanges, GRangesList, GAlignments, or GAlignmentPairs object

Description

coverage methods for GRanges, GRangesList, GAlignments, and GAlignmentPairs objects.

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

Usage

## 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"))

## S4 method for signature 'GAlignments'
coverage(x, shift=0L, width=NULL, weight=1L,
            method=c("auto", "sort", "hash"), drop.D.ranges=FALSE)

## S4 method for signature 'GAlignmentPairs'
coverage(x, shift=0L, width=NULL, weight=1L,
            method=c("auto", "sort", "hash"), drop.D.ranges=FALSE)

Arguments

`x`	A GRanges, GRangesList, GAlignments, or GAlignmentPairs 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.
`drop.D.ranges`	Whether the coverage calculation should ignore ranges corresponding to D (deletion) in the CIGAR string.

Details

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

When x is a GAlignments or GAlignmentPairs object, coverage(x, ...) is equivalent to coverage(grglist(x), ...).

Value

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

Author(s)

H. Pages and P. Aboyoun

Examples

## 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))))

## Coverage of a GAlignments or GAlignmentPairs object:
library(Rsamtools)  # because file ex1.bam is in this package
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn <- readGAlignments(ex1_file)
stopifnot(identical(coverage(galn), coverage(as(galn, "GRangesList"))))
galp <- readGAlignmentPairs(ex1_file)
stopifnot(identical(coverage(galp), coverage(as(galp, "GRangesList"))))

[Package GenomicRanges version 1.14.4 Index]