GNCList-class: GNCList objects
In vjcitn/GenomicRangesGHA: Representation and manipulation of genomic intervals; demo with github actions binary generation

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

The GNCList class is a container for storing the Nested Containment List representation of a vector of genomic ranges (typically represented as a GRanges object). To preprocess a GRanges object, simply call the GNCList constructor function on it. The resulting GNCList object can then be used for efficient overlap-based operations on the genomic ranges.

1	GNCList(x)

`x`	The GRanges (or more generally GenomicRanges) object to preprocess.

The IRanges package also defines the NCList and NCLists constructors and classes for preprocessing and representing a IntegerRanges or IntegerRangesList object as a data structure based on Nested Containment Lists.

Note that GNCList objects (introduced in BioC 3.1) are replacements for GIntervalTree objects (BioC < 3.1).

See ?NCList in the IRanges package for some important differences between the new algorithm based on Nested Containment Lists and the old algorithm based on interval trees. In particular, the new algorithm supports preprocessing of a GenomicRanges object with ranges defined on circular sequences (e.g. on the mitochnodrial chromosome). See below for some examples.

A GNCList object.

H. Pagès

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

The NCList and NCLists constructors and classs defined in the IRanges package.
findOverlaps for finding/counting interval overlaps between two range-based objects.
GRanges objects.

## The examples below are for illustration purpose only and do 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).

## ---------------------------------------------------------------------
## PREPROCESS QUERY OR SUBJECT
## ---------------------------------------------------------------------

query <- GRanges(Rle(c("chrM", "chr1", "chrM", "chr1"), 4:1),
                 IRanges(1:10, width=5), strand=rep(c("+", "-"), 5))
subject <- GRanges(Rle(c("chr1", "chr2", "chrM"), 3:1),
                   IRanges(6:1, width=5), strand="+")

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

ppsubject <- GNCList(subject)
hits1a <- findOverlaps(query, ppsubject)
hits1a
hits1b <- findOverlaps(query, ppsubject, ignore.strand=TRUE)
hits1b

ppquery <- GNCList(query)
hits2a <- findOverlaps(ppquery, subject)
hits2a
hits2b <- findOverlaps(ppquery, subject, ignore.strand=TRUE)
hits2b

## Note that 'hits1a' and 'hits2a' contain the same hits but not
## necessarily in the same order.
stopifnot(identical(sort(hits1a), sort(hits2a)))
## Same for 'hits1b' and 'hits2b'.
stopifnot(identical(sort(hits1b), sort(hits2b)))

## ---------------------------------------------------------------------
## WITH CIRCULAR SEQUENCES
## ---------------------------------------------------------------------

seqinfo <- Seqinfo(c("chr1", "chr2", "chrM"),
                   seqlengths=c(100, 50, 10),
                   isCircular=c(FALSE, FALSE, TRUE))
seqinfo(query) <- seqinfo[seqlevels(query)]
seqinfo(subject) <- seqinfo[seqlevels(subject)]

ppsubject <- GNCList(subject)
hits3 <- findOverlaps(query, ppsubject)
hits3

## Circularity introduces more hits:

stopifnot(all(hits1a %in% hits3))
new_hits <- setdiff(hits3, hits1a)
new_hits  # 1 new hit
query[queryHits(new_hits)]
subject[subjectHits(new_hits)]  # positions 11:13 on chrM are the same
                                # as positions 1:3

## Sanity checks:
stopifnot(identical(new_hits, Hits(9, 6, 10, 6, sort.by.query=TRUE)))
ppquery <- GNCList(query)
hits4 <- findOverlaps(ppquery, subject)
stopifnot(identical(sort(hits3), sort(hits4)))