IRanges (version 2.6.0)

RangesList-class: List of Ranges

Description

An extension of List that holds only Ranges objects. Useful for storing ranges over a set of spaces (e.g. chromosomes), each of which requires a separate Ranges object. As a Vector, RangesList may be annotated with its universe identifier (e.g. a genome) in which all of its spaces exist.

Arithmetic Operations

Any arithmetic operation, such as x + y, x * y, etc, where x is a RangesList, is performed identically on each element. Currently, Ranges supports only the * operator, which zooms the ranges by a numeric factor.

See Also

List, the parent of this class, for more functionality.

Examples

## ---------------------------------------------------------------------
## Basic manipulation
## ---------------------------------------------------------------------

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

# edit the width of the ranges in the list
edited <- named
width(edited) <- rep(c(3,2), elementNROWS(named))
edited

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

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

# set the universe
universe(named) <- "hg18"
universe(named)
RangesList(range1, range2, universe = "hg18")

## zoom in 2X
collection <- RangesList(one = range1, range2)
collection * 2