GenomicAlignments (version 1.2.2)

setops-methods: Set operations on GAlignments objects

Description

Performs set operations on GAlignments objects.

Usage

"pintersect"(x, y, ...)
"pintersect"(x, y, ...)

Arguments

x, y

A GAlignments object and a GRanges object. They must have the same length.

...

Further arguments to be passed to or from other methods.

Value

A GAlignments object parallel to (i.e. same length as) x and y.

See Also

• The GAlignments class.

• The setops-methods man page in the GenomicRanges package.

Examples

## Parallel intersection of a GAlignments and a GRanges object:
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools")
gal <- readGAlignments(bamfile)
pintersect(gal, shift(as(gal, "GRanges"), 6L))