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Last data update: 2014.03.03

R: Coverage of a GRanges or GRangesList object

coverage-methods

R Documentation

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

## 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<c3><83><c2><a8>s 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))))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GenomicRanges)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicRanges/coverage-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverage-methods
> ### Title: Coverage of a GRanges or GRangesList object
> ### Aliases: coverage-methods coverage coverage,GenomicRanges-method
> ###   coverage,GRangesList-method
> ### Keywords: methods utilities
> 
> ### ** 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))))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>