R: Finding overlapping ranges

findOverlaps-methods {IRanges}

R Documentation

Finding overlapping ranges

Description

Various methods for finding/counting interval overlaps between two "range-based" objects: a query and a subject.

NOTE: This man page describes the methods that operate on Ranges, Views, RangesList, or ViewsList objects. See ?`findOverlaps,GenomicRanges,GenomicRanges-method` in the GenomicRanges package for methods that operate on GenomicRanges or GRangesList objects.

Usage

findOverlaps(query, subject, maxgap=-1L, minoverlap=0L,
             type=c("any", "start", "end", "within", "equal"),
             select=c("all", "first", "last", "arbitrary"),
             ...)

countOverlaps(query, subject, maxgap=-1L, minoverlap=0L,
              type=c("any", "start", "end", "within", "equal"),
              ...)

overlapsAny(query, subject, maxgap=-1L, minoverlap=0L,
            type=c("any", "start", "end", "within", "equal"),
            ...)
query %over% subject
query %within% subject
query %outside% subject

subsetByOverlaps(x, ranges, maxgap=-1L, minoverlap=0L,
                 type=c("any", "start", "end", "within", "equal"),
                 invert=FALSE,
                 ...)

overlapsRanges(query, subject, hits=NULL, ...)

poverlaps(query, subject, maxgap = 0L, minoverlap = 1L,
          type = c("any", "start", "end", "within", "equal"),
          ...)

mergeByOverlaps(query, subject, ...)

findOverlapPairs(query, subject, ...)

Arguments

`query, subject, x, ranges`	Each of them can be a Ranges, Views, RangesList, or ViewsList object. In addition, if `subject` or `ranges` is a Ranges object, `query` or `x` can be an integer vector to be converted to length-one ranges. If `query` (or `x`) is a RangesList object, then `subject` (or `ranges`) must also be a RangesList object. If both arguments are list-like objects with names, each list element from the 2nd argument is paired with the list element from the 1st argument with the matching name, if any. Otherwise, list elements are paired by position. The overlap is then computed between the pairs as described below. If `subject` is omitted, `query` is queried against itself. In this case, and only this case, the `drop.self` and `drop.redundant` arguments are allowed. By default, the result will contain hits for each range against itself, and if there is a hit from A to B, there is also a hit for B to A. If `drop.self` is `TRUE`, all self matches are dropped. If `drop.redundant` is `TRUE`, only one of A->B and B->A is returned.
`maxgap`	A single integer >= -1. If `type` is set to `"any"`, `maxgap` is interpreted as the maximum gap that is allowed between 2 ranges for the ranges to be considered as overlapping. The gap between 2 ranges is the number of positions that separate them. The gap between 2 adjacent ranges is 0. By convention when one range has its start or end strictly inside the other (i.e. non-disjoint ranges), the gap is considered to be -1. If `type` is set to anything else, `maxgap` has a special meaning that depends on the particular `type`. See `type` below for more information.
`minoverlap`	A single non-negative integer. Only ranges with a minimum of `minoverlap` overlapping positions are considered to be overlapping. When `type` is `"any"`, at least one of `maxgap` and `minoverlap` must be set to its default value.
`type`	By default, any overlap is accepted. By specifying the `type` parameter, one can select for specific types of overlap. The types correspond to operations in Allen's Interval Algebra (see references). If `type` is `start` or `end`, the intervals are required to have matching starts or ends, respectively. Specifying `equal` as the type returns the intersection of the `start` and `end` matches. If `type` is `within`, the query interval must be wholly contained within the subject interval. Note that all matches must additionally satisfy the `minoverlap` constraint described above. The `maxgap` parameter has special meaning with the special overlap types. For `start`, `end`, and `equal`, it specifies the maximum difference in the starts, ends or both, respectively. For `within`, it is the maximum amount by which the subject may be wider than the query. If `maxgap` is set to -1 (the default), it's replaced internally by 0.
`select`	If `query` is a Ranges or Views object: When `select` is `"all"` (the default), the results are returned as a Hits object. Otherwise the returned value is an integer vector parallel to `query` (i.e. same length) containing the first, last, or arbitrary overlapping interval in `subject`, with `NA` indicating intervals that did not overlap any intervals in `subject`. If `query` is a RangesList or ViewsList object: When `select` is `"all"` (the default), the results are returned as a HitsList object. Otherwise the returned value depends on the `drop` argument. When `select != "all" && !drop`, an IntegerList is returned, where each element of the result corresponds to a space in `query`. When `select != "all" && drop`, an integer vector is returned containing indices that are offset to align with the unlisted `query`.
`invert`	If `TRUE`, keep only the ranges in `x` that do not overlap `ranges`.
`hits`	The Hits or HitsList object returned by `findOverlaps`, or `NULL`. If `NULL` then `hits` is computed by calling `findOverlaps(query, subject, ...)` internally (the extra arguments passed to `overlapsRanges` are passed to `findOverlaps`).
`...`	Further arguments to be passed to or from other methods: `drop`: Supported only when `query` is a RangesList or ViewsList object. `FALSE` by default. See `select` argument above for the details. `drop.self`, `drop.redundant`: When `subject` is omitted, the `drop.self` and `drop.redundant` arguments (both `FALSE` by default) are allowed. See `query` and `subject` arguments above for the details.

Details

A common type of query that arises when working with intervals is finding which intervals in one set overlap those in another.

The simplest approach is to call the findOverlaps function on a Ranges or other object with range information (aka "range-based object").

Value

For findOverlaps: see select argument above.

For countOverlaps: the overlap hit count for each range in query using the specified findOverlaps parameters. For RangesList objects, it returns an IntegerList object.

overlapsAny finds the ranges in query that overlap any of the ranges in subject. For Ranges or Views objects, it returns a logical vector of length equal to the number of ranges in query. For RangesList or ViewsList objects, it returns a LogicalList object where each element of the result corresponds to a space in query.

%over% and %within% are convenience wrappers for the 2 most common use cases. Currently defined as `%over%` <- function(query, subject) overlapsAny(query, subject) and `%within%` <- function(query, subject) overlapsAny(query, subject, type="within"). %outside% is simply the inverse of %over%.

subsetByOverlaps returns the subset of x that has an overlap hit with a range in ranges using the specified findOverlaps parameters.

When hits is a Hits (or HitsList) object, overlapsRanges(query, subject, hits) returns a Ranges (or RangesList) object of the same shape as hits holding the regions of intersection between the overlapping ranges in objects query and subject, which should be the same query and subject used in the call to findOverlaps that generated hits. Same shape means same length when hits is a Hits object, and same length and same elementNROWS when hits is a HitsList object.

poverlaps compares query and subject in parallel (like e.g., pmin) and returns a logical vector indicating whether each pair of ranges overlaps. Integer vectors are treated as width-one ranges.

mergeByOverlaps computes the overlap between query and subject according to the arguments in .... It then extracts the corresponding hits from each object and returns a DataFrame containing one column for the query and one for the subject, as well as any mcols that were present on either object. The query and subject columns are named by quoting and deparsing the corresponding argument.

findOverlapPairs is like mergeByOverlaps, except it returns a formal Pairs object that provides useful downstream conveniences, such as finding the intersection of the overlapping ranges with pintersect.

Author(s)

Michael Lawrence and Hervé Pagès

References

Allen's Interval Algebra: James F. Allen: Maintaining knowledge about temporal intervals. In: Communications of the ACM. 26/11/1983. ACM Press. S. 832-843, ISSN 0001-0782

Examples

## ---------------------------------------------------------------------
## findOverlaps()
## ---------------------------------------------------------------------

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

findOverlaps(query, subject)

## at most one hit per query
findOverlaps(query, subject, select="first")
findOverlaps(query, subject, select="last")
findOverlaps(query, subject, select="arbitrary")

## including adjacent ranges in the result
findOverlaps(query, subject, maxgap=0L)

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

## one IRanges object with itself
findOverlaps(query)

## single points as query
subject <- IRanges(c(1, 6, 13), c(4, 9, 14))
findOverlaps(c(3L, 7L, 10L), subject, select="first")

## special overlap types
query <- IRanges(c(1, 5, 3, 4), width=c(2, 2, 4, 6))
subject <- IRanges(c(1, 3, 5, 6), width=c(4, 4, 5, 4))

findOverlaps(query, subject, type="start")
findOverlaps(query, subject, type="start", maxgap=1L)
findOverlaps(query, subject, type="end", select="first")
ov <- findOverlaps(query, subject, type="within", maxgap=1L)
ov

## Using pairs to find intersection of overlapping ranges
hits <- findOverlaps(query, subject)
p <- Pairs(query, subject, hits=hits)
pintersect(p)

## Shortcut
p <- findOverlapPairs(query, subject)
pintersect(p)

## ---------------------------------------------------------------------
## overlapsAny()
## ---------------------------------------------------------------------

overlapsAny(query, subject, type="start")
overlapsAny(query, subject, type="end")
query %over% subject    # same as overlapsAny(query, subject)
query %within% subject  # same as overlapsAny(query, subject,
                          #                     type="within")

## ---------------------------------------------------------------------
## overlapsRanges()
## ---------------------------------------------------------------------

## Extract the regions of intersection between the overlapping ranges:
overlapsRanges(query, subject, ov)

## ---------------------------------------------------------------------
## Using RangesList objects
## ---------------------------------------------------------------------

query <- IRanges(c(1, 4, 9), c(5, 7, 10))
qpartition <- factor(c("a","a","b"))
qlist <- split(query, qpartition)

subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
spartition <- factor(c("a","a","b"))
slist <- split(subject, spartition)

## at most one hit per query
findOverlaps(qlist, slist, select="first")
findOverlaps(qlist, slist, select="last")
findOverlaps(qlist, slist, select="arbitrary")

query <- IRanges(c(1, 5, 3, 4), width=c(2, 2, 4, 6))
qpartition <- factor(c("a","a","b","b"))
qlist <- split(query, qpartition)

subject <- IRanges(c(1, 3, 5, 6), width=c(4, 4, 5, 4))
spartition <- factor(c("a","a","b","b"))
slist <- split(subject, spartition)

overlapsAny(qlist, slist, type="start")
overlapsAny(qlist, slist, type="end")
qlist 

subsetByOverlaps(qlist, slist)
countOverlaps(qlist, slist)

[Package IRanges version 2.12.0 Index]