| RangesList-class {IRanges} | R Documentation |
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.
In the code snippets below, x is a RangesList
object.
All of these accessors collapse over the spaces:
start(x), start(x) <- value: Get or set the starts of the
ranges. When setting the starts, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
end(x), end(x) <- value: Get or set the ends of the
ranges. When setting the ends, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
width(x), width(x) <- value: Get or set the widths of the
ranges. When setting the widths, value can be an integer vector
of length sum(elementNROWS(x)) or an IntegerList object of
length length(x) and names names(x).
space(x): Gets the spaces of the ranges as a
character vector. This is equivalent to names(x), except each
name is repeated according to the length of its element.
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.
In the code snippet below, x is a RangesList object.
as.data.frame(x, row.names = NULL, optional = FALSE,
..., value.name = "value", use.outer.mcols = FALSE,
group_name.as.factor = FALSE):
Coerces x to a data.frame. See as.data.frame on the
List man page for details (?List).
In the following code snippet, from is something other than a
RangesList:
as(from, "RangesList"): When from is a
Ranges, analogous to as.list on a vector.
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.
Michael Lawrence
List, the parent of this class, for more
functionality.
## --------------------------------------------------------------------- ## 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) RangesList(range1, range2) ## zoom in 2X collection <- RangesList(one = range1, range2) collection * 2