range-squeezers

Squeeze the ranges out of a range-based object

S4 generic functions for squeezing the ranges out of a range-based object.

granges returns them as a GRanges object, grglist as a GRangesList object, and rglist as a RangesList object.

Keywords
methods
Usage
granges(x, use.mcols=FALSE, ...) grglist(x, use.mcols=FALSE, ...) rglist(x, use.mcols=FALSE, ...)
Arguments
x
A range-based object e.g. a RangedSummarizedExperiment, GAlignments, GAlignmentPairs, GAlignmentsList or a Pairs object containing ranges.
use.mcols
TRUE or FALSE (the default). Whether the metadata columns on x (accessible with mcols(x)) should be propagated to the returned object or not.
...
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), as(x, "GRanges"), as(x, "GRangesList"), and as(x, "RangesList"), are equivalent to granges(x, use.mcols=TRUE), grglist(x, use.mcols=TRUE), and rglist(x, 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 x has names on it, they're propagated to the returned object. If use.mcols is TRUE and x has metadata columns on it (accessible with mcols(x)), they're propagated to the returned object.

See Also

Aliases
  • range-squeezers
  • granges
  • grglist
  • rglist
  • grglist,Pairs-method
  • rglist,Pairs-method
Examples
## See ?GAlignments in the GenomicAlignments package for some
## examples.
Documentation reproduced from package GenomicRanges, version 1.24.1, License: Artistic-2.0

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