coverage-methods {GenomicAlignments}R Documentation

Coverage of a GAlignments or GAlignmentPairs object

Description

coverage methods for GAlignments, GAlignmentPairs, and BamFile objects.

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

Usage

## 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)

## S4 method for signature 'BamFile'
coverage(x, shift=0L, width=NULL, weight=1L, ...,
         param=ScanBamParam())

## S4 method for signature 'character'
coverage(x, shift=0L, width=NULL, weight=1L, ...,
         yieldSize=2500000L)

Arguments

x

A GAlignments, GAlignmentPairs, BamFile or character(1) object.

shift, width, weight

See coverage method for GRanges objects in the GenomicRanges package.

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.

...

Additional arguments passed to the coverage method for GAlignments objects.

param

An optional ScanBamParam object passed to readGAlignments.

yieldSize

An optional argument controlling how many records are input when iterating through a BamFile.

Details

The methods for GAlignments and GAlignmentPairs objects do: 

  coverage(grglist(x), ...)

The method for BamFile objects iterates through a BAM file, reading yieldSize(x) records (or all records, if is.na(yieldSize(x))) and calculating: 

  aln <- readGAlignments(x, param=param)
  coverage(aln, shift=shift, width=width, weight=weight, ...)

The method for character vectors of length 1 creates a BamFile object from x and performs the calculation for coverage,BamFile-method.

Value

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

See Also

Examples

ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")

gal <- readGAlignments(ex1_file)
stopifnot(identical(coverage(gal), coverage(as(gal, "GRangesList"))))

galp <- readGAlignmentPairs(ex1_file)
stopifnot(identical(coverage(galp), coverage(as(galp, "GRangesList"))))
[Package GenomicAlignments version 1.4.1 Index]