IRanges-setops {IRanges}R Documentation

Set operations on IRanges objects

Description

Performs set operations on IRanges objects.

Usage

  ## Vector-wise operations:
  ## S4 method for signature 'IRanges, IRanges':
  union(x, y)
  ## S4 method for signature 'IRanges, IRanges':
  intersect(x, y)
  ## S4 method for signature 'IRanges, IRanges':
  setdiff(x, y)

  ## Element-wise (aka "parallel") operations:
  punion(x, y, ...)
  pintersect(x, y, ...)
  psetdiff(x, y, ...)
  pgap(x, y, ...)

Arguments

x, y IRanges objects.
... Further arguments to be passed to or from other methods. For example, the fill.gap argument can be passed to the punion method for IRanges objects (see below).

Details

The union, intersect and setdiff methods for IRanges objects return a "normal" IRanges object (of the same class as x) 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 IRanges objects are defined. For these methods, x and y must have the same length (i.e. same number of ranges) and they return an IRanges instance of the same length as x and y where each range represents the union/intersection/difference/gap of/between the corresponding ranges in x and y.

Note that the union or difference of 2 ranges cannot always be represented by a single range so punion and psetdiff cannot always return their result in an IRanges instance of the same length as the input. This happens to punion when there is a gap between the 2 ranges to combine. In that case, the user can use the fill.gap argument to enforce the union by filling the gap. This happens to psetdiff when a range in y has its end points strictly inside the corresponding range in x. In that case, psetdiff will simply fail.

If two ranges overlap, then the gap between them is empty.

Author(s)

H. Pages and M. Lawrence

See Also

Ranges-class, IRanges-class, IRanges-utils

Examples

  x <- IRanges(c(1, 5, -2, 0, 14), c(10, 9, 3, 11, 17))
  y <- Views(as(4:-17, "XInteger"), start=c(14, 0, -5, 6, 18), end=c(20, 2, 2, 8, 20))

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

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

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

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

[Package IRanges version 1.2.3 Index]