Squeeze the ranges out of a range-based object

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Description

S4 generic functions for squeezing the ranges out of a range-based object. granges returns them in a GRanges object, grglist in a GRangesList object, and rglist in a RangesList object.

Usage

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granges(x, use.names=TRUE, use.mcols=FALSE, ...)
grglist(x, use.names=TRUE, use.mcols=FALSE, ...)
rglist(x, use.names=TRUE, use.mcols=FALSE, ...)

Arguments

x

A range-based object e.g. a RangedSummarizedExperiment, GAlignments, GAlignmentPairs, GAlignmentsList or a Pairs object containing ranges.

use.names

TRUE (the default) or FALSE. Whether or not the names on x (accessible with names(x)) should be propagated to the returned object.

use.mcols

TRUE or FALSE (the default). Whether or not the metadata columns on x (accessible with mcols(x)) should be propagated to the returned object.

...

Additional arguments, for use in specific methods.

Details

The GenomicRanges, SummarizedExperiment, and GenomicAlignments packages define and document methods for various types of range-based objects (e.g. for RangedSummarizedExperiment, GAlignments, GAlignmentPairs, and GAlignmentsList objects). Other Bioconductor packages might as well.

Note that these functions can be seen as a specific kind of object getters as well as functions performing coercion.

For some objects (e.g. GAlignments and GAlignmentPairs objects defined in the GenomicAlignments package), as(x, "GRanges"), as(x, "GRangesList"), and as(x, "RangesList"), are equivalent to granges(x, use.names=TRUE, use.mcols=TRUE), grglist(x, use.names=TRUE, use.mcols=TRUE), and rglist(x, use.names=TRUE, use.mcols=TRUE), respectively.

Value

A GRanges object for granges.

A GRangesList object for grglist.

A RangesList object for rglist.

If x is a vector-like object (e.g. GAlignments), the returned object is expected to be parallel to x, that is, the i-th element in the output corresponds to the i-th element in the input.

If use.names is TRUE, then the names on x (if any) are propagated to the returned object. If use.mcols is TRUE, then the metadata columns on x (if any) are propagated to the returned object.

Author(s)

H. Pag├Ęs

See Also

  • GRanges and GRangesList objects.

  • RangesList objects in the IRanges package.

  • RangedSummarizedExperiment objects in the SummarizedExperiment packages.

  • GAlignments, GAlignmentPairs, and GAlignmentsList objects in the GenomicAlignments package.

Examples

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## See ?GAlignments in the GenomicAlignments package for some
## examples.