NCList-class {IRanges} | R Documentation

## Nested Containment List objects

### Description

The NCList class is a container for storing the Nested Containment List representation of a IntegerRanges object. Preprocessing a IntegerRanges object as a Nested Containment List allows efficient overlap-based operations like `findOverlaps`.

The NCLists class is a container for storing a collection of NCList objects. An NCLists object is typically the result of preprocessing each list element of a IntegerRangesList object as a Nested Containment List. Like with NCList, the NCLists object can then be used for efficient overlap-based operations.

To preprocess a IntegerRanges or IntegerRangesList object, simply call the `NCList` or `NCLists` constructor function on it.

### Usage

    NCList(x, circle.length=NA_integer_)
    NCLists(x, circle.length=NA_integer_)

### Arguments

`x` | The IntegerRanges or IntegerRangesList object to preprocess.
`circle.length` | Use only if the space (or spaces if `x` is a IntegerRangesList object) on top of which the ranges in `x` are defined needs (need) to be considered circular. If that's the case, then use `circle.length` to specify the length(s) of the circular space(s). For `NCList`, `circle.length` must be a single positive integer (or NA if the space is linear). For `NCLists`, it must be an integer vector parallel to `x` (i.e. same length) and with positive or NA values (NAs indicate linear spaces).

### Details

The GenomicRanges package also defines the `GNCList` constructor and class for preprocessing and representing a vector of genomic ranges as a data structure based on Nested Containment Lists.

Some important differences between the new findOverlaps/countOverlaps implementation based on Nested Containment Lists (BioC >= 3.1) and the old implementation based on Interval Trees (BioC < 3.1):

- With the new implementation, the hits returned by `findOverlaps` are not fully ordered (i.e. ordered by queryHits and subject Hits) anymore, but only partially ordered (i.e. ordered by queryHits only). Other than that, and except for the 2 particular situations mentioned below, the 2 implementations produce the same output. However, the new implementation is faster and more memory efficient.

- With the new implementation, either the query or the subject can be preprocessed with `NCList` for a IntegerRanges object (replacement for `IntervalTree`), `NCLists` for a IntegerRangesList object (replacement for `IntervalForest`), and `GNCList` for a GenomicRanges object (replacement for `GIntervalTree`). However, for a one-time use, it is NOT advised to explicitely preprocess the input. This is because `findOverlaps` or `countOverlaps` will take care of it and do a better job at it (by preprocessing only what's needed when it's needed, and releasing memory as they go).

- With the new implementation, `countOverlaps` on IntegerRanges or GenomicRanges objects doesn't call `findOverlaps` in order to collect all the hits in a growing Hits object and count them only at the end. Instead, the counting happens at the C level and the hits are not kept. This reduces memory usage considerably when there is a lot of hits.

- When `minoverlap=0`, zero-width ranges are now interpreted as insertion points and considered to overlap with ranges that contain them. With the old alogrithm, zero-width ranges were always ignored. This is the 1st situation where the new and old implementations produce different outputs.

- When using `select="arbitrary"`, the new implementation will generally not select the same hits as the old implementation. This is the 2nd situation where the new and old implementations produce different outputs.

- The new implementation supports preprocessing of a GenomicRanges object with ranges defined on circular sequences (e.g. on the mitochnodrial chromosome). See GNCList in the GenomicRanges package for some examples.

- Objects preprocessed with `NCList`, `NCLists`, and `GNCList` are serializable (with `save`) for later use. Not a typical thing to do though, because preprocessing is very cheap (i.e. very fast and memory efficient).

### Value

An NCList object for the `NCList` constructor and an NCLists object for the `NCLists` constructor.

### Author(s)

Hervé Pagès

### References

Alexander V. Alekseyenko and Christopher J. Lee – Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics (2007) 23 (11): 1386-1393. doi: 10.1093/bioinformatics/btl647

### See Also

- The `GNCList` constructor and class defined in the GenomicRanges package.

- `findOverlaps` for finding/counting interval overlaps between two range-based objects.

- IntegerRanges and IntegerRangesList objects.

### Examples

    ## The example below is for illustration purpose only and does NOT
    ## reflect typical usage. This is because, for a one-time use, it is
    ## NOT advised to explicitely preprocess the input for findOverlaps()
    ## or countOverlaps(). These functions will take care of it and do a
    ## better job at it (by preprocessing only what's needed when it's
    ## needed, and release memory as they go).

    query <- IRanges(c(1, 4, 9), c(5, 7, 10))
    subject <- IRanges(c(2, 2, 10), c(2, 3, 12))

    ## Either the query or the subject of findOverlaps() can be preprocessed:

    ppsubject <- NCList(subject)
    hits1 <- findOverlaps(query, ppsubject)
    hits1

    ppquery <- NCList(query)
    hits2 <- findOverlaps(ppquery, subject)
    hits2

    ## Note that 'hits1' and 'hits2' contain the same hits but not in the
    ## same order.
    stopifnot(identical(sort(hits1), sort(hits2)))

[Package IRanges version 2.26.0 Index]