setops-methods {GenomicAlignments} | R Documentation

## Set operations on GAlignments objects

### Description

Performs set operations on GAlignments objects.

NOTE: The `pintersect` generic function and method for IntegerRanges objects is 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,GRanges'
    pintersect(x, y, ...)
    ## S4 method for signature 'GRanges,GAlignments'
    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))

[Package GenomicAlignments version 1.16.0 Index]