IRanges (version 2.2.9)

IntervalForest-class: Interval Search Forests

Description

Efficiently perform overlap queries with a set of interval trees.

WARNING: IntervalForest objects are deprecated. Please use NCLists objects instead. See ?NCLists for more information.

Constructor

IntervalForest(rangesList): Creates an IntervalForest from the ranges list in rangesList, an object coercible to CompressedIRangesList.

Accessors

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.

Details

A common type of query that arises when working with intervals is finding which intervals in one set overlap those in another. An efficient family of algorithms for answering such queries is known as the Interval Tree. The 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.

See Also

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.

Examples

if (interactive()) {
  ## IntervalForest objects are deprecated. Please use NCLists objects
  ## instead. See ?NCLists for more information.
  query <- IRangesList(a=IRanges(c(1,4),c(5,7)),b=IRanges(9,10))
  subject <- IRangesList(a=IRanges(c(2,2),c(2,3)),b=IRanges(10,12))
  forest <- IntervalForest(subject)

  findOverlaps(query, forest)
}