GenomicRanges (version 1.24.1)

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.


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


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


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.


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.

See Also


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

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