RangesList-utils {IRanges}R Documentation

RangesList utility functions

Description

Utility functions for manipulating RangesList objects.

Usage

## S4 method for signature 'RangesList':
gaps(x, start=NA, end=NA)
## S4 method for signature 'RangesList':
reduce(x, with.inframe.attrib = FALSE)

Arguments

x A RangesList
start The start of the range over which to calculate the gaps. If NA, use the minimum start position in the Ranges instance.
end The end of the range over which to calculate the gaps. If NA, use the maximum end position in the Ranges instance.
with.inframe.attrib Ignored.

Details

The gaps function takes the complement (the gaps) of each element in the list and returns the result as a RangesList.

The reduce method merges (via reduce) all of the elements into a single Ranges instance and returns the result as a length-one RangesList.

Value

A RangesList instance. For gaps, length is the same as that of x. For reduce, length is one.

Author(s)

Michael Lawrence, H. Pages

See Also

RangesList, reduce, gaps

Examples

  # 'gaps'
  range1 <- IRanges(start=c(1,2,3), end=c(5,2,8))
  range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
  collection <- RangesList(one = range1, range2)

  # these two are the same
  RangesList(gaps(range1), gaps(range2))
  gaps(collection)

  # 'reduce'
  range2 <- IRanges(start=c(45,20,1), end=c(100,80,5))
  collection <- RangesList(one = range1, range2)

  # and these two are the same
  reduce(collection)
  RangesList(asNormalIRanges(IRanges(c(1,20), c(8, 100)), force=FALSE))

[Package IRanges version 1.0.16 Index]