setops-methods: Set operations on IntegerRanges and IntegerRangesList objects

In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

Set operations on IntegerRanges and IntegerRangesList objects

Description

Performs set operations on IntegerRanges and IntegerRangesList objects.

Usage

## Vector-wise set operations
## --------------------------

## S4 method for signature 'IntegerRanges,IntegerRanges'
union(x, y)
## S4 method for signature 'Pairs,missing'
union(x, y, ...)

## S4 method for signature 'IntegerRanges,IntegerRanges'
intersect(x, y)
## S4 method for signature 'Pairs,missing'
intersect(x, y, ...)

## S4 method for signature 'IntegerRanges,IntegerRanges'
setdiff(x, y)
## S4 method for signature 'Pairs,missing'
setdiff(x, y, ...)

## Element-wise (aka "parallel") set operations
## --------------------------------------------

## S4 method for signature 'IntegerRanges,IntegerRanges'
punion(x, y, fill.gap=FALSE)
## S4 method for signature 'Pairs,missing'
punion(x, y, ...)

## S4 method for signature 'IntegerRanges,IntegerRanges'
pintersect(x, y, resolve.empty=c("none", "max.start", "start.x"))
## S4 method for signature 'Pairs,missing'
pintersect(x, y, ...)

## S4 method for signature 'IntegerRanges,IntegerRanges'
psetdiff(x, y)
## S4 method for signature 'Pairs,missing'
psetdiff(x, y, ...)

## S4 method for signature 'IntegerRanges,IntegerRanges'
pgap(x, y)

Arguments

x, y	Objects representing ranges.
fill.gap	Logical indicating whether or not to force a union by using the rule start = min(start(x), start(y)), end = max(end(x), end(y)).
resolve.empty	One of "none", "max.start", or "start.x" denoting how to handle ambiguous empty ranges formed by intersections. "none" - throw an error if an ambiguous empty range is formed, "max.start" - associate the maximum start value with any ambiguous empty range, and "start.x" - associate the start value of x with any ambiguous empty range. (See Details section below for the definition of an ambiguous range.)
...	The methods for Pairs objects pass any extra argument to the internal call to punion(first(x), last(x), ...), pintersect(first(x), last(x), ...), etc...

Details

The union, intersect and setdiff methods for IntegerRanges objects return a "normal" IntegerRanges object representing the union, intersection and (asymmetric!) difference of the sets of integers represented by x and y.

punion, pintersect, psetdiff and pgap are generic functions that compute the element-wise (aka "parallel") union, intersection, (asymmetric!) difference and gap between each element in x and its corresponding element in y. Methods for IntegerRanges objects are defined. For these methods, x and y must have the same length (i.e. same number of ranges). They return a IntegerRanges object parallel to x and y i.e. where the i-th range corresponds to the i-th range in x and iny) and represents the union/intersection/difference/gap of/between the corresponding x[i] and y[i].

If x is a Pairs object, then y should be missing, and the operation is performed between the members of each pair.

By default, pintersect will throw an error when an "ambiguous empty range" is formed. An ambiguous empty range can occur three different ways: 1) when corresponding non-empty ranges elements x and y have an empty intersection, 2) if the position of an empty range element does not fall within the corresponding limits of a non-empty range element, or 3) if two corresponding empty range elements do not have the same position. For example if empty range element [22,21] is intersected with non-empty range element [1,10], an error will be produced; but if it is intersected with the range [22,28], it will produce [22,21]. As mentioned in the Arguments section above, this behavior can be changed using the resolve.empty argument.

Value

On IntegerRanges objects, union, intersect, and setdiff return an IRanges instance that is guaranteed to be normal (see isNormal) but is NOT promoted to NormalIRanges.

On IntegerRanges objects, punion, pintersect, psetdiff, and pgap return an object of the same class and length as their first argument.

Author(s)

H. Pagès and M. Lawrence

See Also

• pintersect is similar to narrow, except the end points are absolute, not relative. pintersect is also similar to restrict, except ranges outside of the restriction become empty and are not discarded.

• setops-methods in the GenomicRanges package for set operations on genomic ranges.

• findOverlaps-methods for finding/counting overlapping ranges.

• intra-range-methods and inter-range-methods for intra range and inter range transformations.

• IntegerRanges and IntegerRangesList objects. In particular, normality of an IntegerRanges object is discussed in the man page for IntegerRanges objects.

• mendoapply in the S4Vectors package.

Examples

x <- IRanges(c(1, 5, -2, 0, 14), c(10, 9, 3, 11, 17))
subject <- Rle(1:-3, 6:2)
y <- Views(subject, start=c(14, 0, -5, 6, 18), end=c(20, 2, 2, 8, 20))

## Vector-wise operations:
union(x, ranges(y))
union(ranges(y), x)

intersect(x, ranges(y))
intersect(ranges(y), x)

setdiff(x, ranges(y))
setdiff(ranges(y), x)

## Element-wise (aka "parallel") operations:
try(punion(x, ranges(y)))
punion(x[3:5], ranges(y)[3:5])
punion(x, ranges(y), fill.gap=TRUE)
try(pintersect(x, ranges(y)))
pintersect(x[3:4], ranges(y)[3:4])
pintersect(x, ranges(y), resolve.empty="max.start")
psetdiff(ranges(y), x)
try(psetdiff(x, ranges(y)))
start(x)[4] <- -99
end(y)[4] <- 99
psetdiff(x, ranges(y))
pgap(x, ranges(y))

## On IntegerRangesList objects:
irl1 <- IRangesList(a=IRanges(c(1,2),c(4,3)), b=IRanges(c(4,6),c(10,7)))
irl2 <- IRangesList(c=IRanges(c(0,2),c(4,5)), a=IRanges(c(4,5),c(6,7)))
union(irl1, irl2)
intersect(irl1, irl2)
setdiff(irl1, irl2)

Bioconductor/IRanges documentation built on Dec. 7, 2024, 1:19 p.m.