WARNING: IntervalForest objects are defunct. Please use NCLists
objects instead. See ?NCLists
for more information.
IntervalForest
from the
ranges list in rangesList
, an object coercible to
CompressedIRangesList
.
length(x)
: Gets the number of ranges stored in the
forest. This is a fast operation that does not bring the ranges into
R.start(x)
: Get the starts of the ranges as a CompressedIntegerList
.end(x)
: Get the ends of the ranges as CompressedIntegerList
.x@partitioning
: The range partitioning of class PartitioningByEnd
.names(x)
: Get the names of the range partitioning.elementLengths(x)
: The number of ranges in each partition.IntervalForest
class stores a set of Interval Trees
corresponding to intervals that are partitioned into disjoint sets. The most
efficient way to construct IntervalForest
objects is to call the constructor below
on a CompressedIRangesList object. See the IntervalTree class for the
underlying Interval Tree data structure. A canonical example of a compressed ranges list are GenomicRanges
objects, where intervals are partitioned by their seqnames
. See the
GIntervalTree class to see the use of IntervalForest
objects
in this case.
The simplest approach for finding overlaps is to call the
findOverlaps
function on a RangesList object.
See the man page of findOverlaps-methods
for how to use this and other related functions.
findOverlaps-methods
for finding/counting interval overlaps between
two compressed lists of "range-based" objects,
RangesList
, the parent of this class,
CompressedHitsList
, set of hits between 2 list-like objects,
GIntervalTree
, which uses IntervalForest
objects.
## IntervalForest objects are defunct. Please use NCLists objects
## instead. See ?NCLists for more information.
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