Squeeze the genomic ranges out of a range-based object
S4 generic functions for squeezing the genomic ranges out of a range-based object.
These are analog to range squeezers ranges and
rglist defined in the IRanges package, except
that granges returns the ranges in a GRanges object (instead
of an IRanges object for ranges),
and grglist returns them in a GRangesList object (instead of
an IRangesList object for rglist).
granges(x, use.names=TRUE, use.mcols=FALSE, ...) grglist(x, use.names=TRUE, use.mcols=FALSE, ...)
x |
An object containing genomic ranges e.g. a GenomicRanges, RangedSummarizedExperiment, GAlignments, GAlignmentPairs, or GAlignmentsList object, or a Pairs object containing genomic ranges. |
use.names, use.mcols, ... |
See |
See ranges in the IRanges package for
some details.
For some objects (e.g. GAlignments and
GAlignmentPairs objects defined in the
GenomicAlignments package), as(x, "GRanges") and
as(x, "GRangesList"), are equivalent to
granges(x, use.names=TRUE, use.mcols=TRUE) and
grglist(x, use.names=TRUE, use.mcols=TRUE), respectively.
A GRanges object for granges.
A GRangesList object for grglist.
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.
H. Pagès
GRanges and GRangesList objects.
RangedSummarizedExperiment objects in the SummarizedExperiment packages.
GAlignments, GAlignmentPairs, and GAlignmentsList objects in the GenomicAlignments package.
## See ?GAlignments in the GenomicAlignments package for examples of ## "ranges" and "rglist" methods.
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