coverage-methods: Coverage of a GRanges or GRangesList object
In GenomicRanges: Representation and manipulation of genomic intervals

Description Usage Arguments Details Value Author(s) See Also Examples

coverage methods for GRanges and GRangesList objects.

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

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

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

`x`	A GenomicRanges or GRangesList object.
`shift, 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, each of these arguments 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` (or `weight`) vector. See `?coverage` in the IRanges package for more information about these arguments. Note that when `x` is a StitchedGPos object, each of these arguments can only be a single number or a named list-like object.
`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.
`method`	See `?coverage` in the IRanges package for a description of this argument.

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

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

H. Pag<c3><a8>s and P. Aboyoun

coverage in the IRanges package.
coverage-methods in the GenomicAlignments package.
RleList objects in the IRanges package.
GRanges, GPos, and GRangesList objects.

## 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 GPos object:
pos_runs <- GRanges(c("chr1", "chr1", "chr2"),
                    IRanges(c(1, 5, 9), c(10, 8, 15)))
gpos <- GPos(pos_runs)
coverage(gpos)

## 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))))

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
RleList of length 2
$chr1
integer-Rle of length 10 with 3 runs
  Lengths: 4 4 2
  Values : 1 2 1

$chr2
integer-Rle of length 15 with 2 runs
  Lengths: 8 7
  Values : 0 1