RangesList-class {IRanges}R Documentation

List of Ranges

Description

An extension of TypedList that holds only Ranges instances. Useful for storing ranges over a set of spaces (e.g. chromosomes), each of which requires a separate Ranges instance.

Accessors

In the code snippets below, x is a RangesList object. All accessors collapse over the spaces.

start(x): Get the starts of the ranges.
end(x): Get the ends of the ranges.
width(x): Get the widths of the ranges.
isEmpty(x): Gets a logical vector indicating which elements are empty (length zero).

Constructor

RangesList(...): Each Ranges in ... becomes an element in the new RangesList, in the same order. This is analogous to the list constructor, except every argument in ... must be derived from Ranges.

Coercion

In the code snippets below, x is a RangesList object.

as.data.frame(x, row.names = NULL, optional = FALSE): Coerces x to a data.frame. Essentially the same as calling as.data.frame(unlist(x)).
as(from, "IRangesList"): Coerces from, a RangesList, to an IRangesList, requiring that all Ranges elements are coerced to internal IRanges elements. This is a convenient way to ensure that all Ranges have been imported into R (and that there is no unwanted overhead when accessing them).

Author(s)

Michael Lawrence

Examples

  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))
  named <- RangesList(one = range1, two = range2)
  length(named) # 2
  start(named) # same as start(c(range1, range2))
  names(named) # "one" and "two"
  named[[1]] # range1
  unnamed <- RangesList(range1, range2)
  names(unnamed) # NULL

  # same as list(range1, range2)
  as.list(RangesList(range1, range2))

  # coerce to data.frame
  as.data.frame(named)

[Package IRanges version 1.0.16 Index]