IntegerRangesList objects
The IntegerRangesList virtual class is a general container for storing a list of IntegerRanges objects.
Most users are probably more interested in the IRangesList container, an IntegerRangesList derivative for storing a list of IRanges objects.
The place of IntegerRangesList in the Vector class hierarchy:
Vector
^
|
List
^
|
RangesList
^ ^
/ \
/ \
/ \
/ \
/ \
/ \
IntegerRangesList GenomicRangesList
^ ^
| |
IRangesList GRangesList
^ ^ ^ ^
/ \ / \
/ \ / \
/ \ / \
SimpleIRangesList \ SimpleGRangesList \
CompressedIRangesList CompressedGRangesListNote that the Vector class hierarchy has many more classes. In particular Vector, List, RangesList, and IntegerRangesList have other subclasses not shown here.
In the code snippets below, x is a IntegerRangesList
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.
In the code snippet below, x is an IntegerRangesList 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
IntegerRangesList:
as(from, "IntegerRangesList"): When from is a
IntegerRanges, analogous to as.list on a vector.
Any arithmetic operation, such as x + y, x * y, etc,
where x is a IntegerRangesList, is performed identically on
each element. Currently, IntegerRanges supports only the *
operator, which zooms the ranges by a numeric factor.
M. Lawrence & H. Pagès
IRangesList objects.
IntegerRanges and IRanges objects.
## --------------------------------------------------------------------- ## 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 <- IRangesList(one = range1, two = range2) length(named) # 2 start(named) # same as start(c(range1, range2)) names(named) # "one" and "two" named[[1]] # range1 unnamed <- IRangesList(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(IRangesList(range1, range2)) # coerce to data.frame as.data.frame(named) IRangesList(range1, range2) ## zoom in 2X collection <- IRangesList(one = range1, range2) collection * 2
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