range-squeezers {GenomicRanges} | R Documentation |
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.
granges(x, use.names=TRUE, use.mcols=FALSE, ...) grglist(x, use.names=TRUE, use.mcols=FALSE, ...) rglist(x, use.names=TRUE, use.mcols=FALSE, ...)
x |
A range-based object e.g. a RangedSummarizedExperiment, GAlignments, GAlignmentPairs, GAlignmentsList or a Pairs object containing ranges. |
use.names |
|
use.mcols |
|
... |
Additional arguments, for use in specific methods. |
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.
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.
H. Pagès
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.
## See ?GAlignments in the GenomicAlignments package for some ## examples.