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, ...)TRUE or FALSE (the default).
Whether the metadata columns on x (accessible with mcols(x))
should be propagated to the returned object or not.
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.
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 ?GAlignments in the GenomicAlignments package for some
## examples.
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