NCList-class: Nested Containment List objects

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

The NCList class is a container for storing the Nested Containment List representation of a Ranges object. Preprocessing a Ranges 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 RangesList object as a Nested Containment List. Like with NCList, the NCLists object can then be used for efficient overlap-based operations.

To preprocess a Ranges or RangesList object, simply call the NCList or NCLists constructor function on it.

Usage

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

Arguments

x

The Ranges or RangesList object to preprocess.

circle.length

Use only if the space (or spaces if x is a RangesList 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):

Value

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

Author(s)

Herv<c3><a9> Pag<c3><a8>s

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

Examples

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## 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)))

IRanges documentation built on Oct. 9, 2017, 2:03 a.m.