## Vector-wise set operations
## --------------------------
"union"(x, y)
"intersect"(x, y)
"setdiff"(x, y)
## Element-wise (aka "parallel") set operations
## --------------------------------------------
"punion"(x, y, fill.gap=FALSE)
"punion"(x, y, ...)
"pintersect"(x, y, resolve.empty=c("none", "max.start", "start.x"))
"pintersect"(x, y, ...)
"psetdiff"(x, y)
"psetdiff"(x, y, ...)
"pgap"(x, y)start = min(start(x), start(y)), end = max(end(x), end(y)).
"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.)
punion(first(x), last(x), ...),
pintersect(first(x), last(x), ...), etc...
union, intersect and setdiff methods
for Ranges objects return a "normal" Ranges
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 Ranges objects are defined. For these methods,
x and y must have the same length (i.e. same number
of ranges). They return a Ranges 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.
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.
mendoapply in the S4Vectors package.
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 RangesList 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)
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