IntegerRangesList-class {IRanges} | R Documentation |
IntegerRangesList objects
Description
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.
Details
The place of IntegerRangesList in the Vector class hierarchy:
Vector ^ | List ^ | RangesList ^ ^ / \ / \ / \ / \ / \ / \ IntegerRangesList GenomicRangesList ^ ^ | | IRangesList GRangesList ^ ^ ^ ^ / \ / \ / \ / \ / \ / \ SimpleIRangesList \ SimpleGRangesList \ CompressedIRangesList CompressedGRangesList
Note that the Vector class hierarchy has many more classes. In particular Vector, List, RangesList, and IntegerRangesList have other subclasses not shown here.
Accessors
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 lengthsum(elementNROWS(x))
or an IntegerList object of lengthlength(x)
and namesnames(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 lengthsum(elementNROWS(x))
or an IntegerList object of lengthlength(x)
and namesnames(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 lengthsum(elementNROWS(x))
or an IntegerList object of lengthlength(x)
and namesnames(x)
.space(x)
: Gets the spaces of the ranges as a character vector. This is equivalent tonames(x)
, except each name is repeated according to the length of its element.
Coercion
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)
: Coercesx
to adata.frame
. See as.data.frame on theList
man page for details (?List
).
In the following code snippet, from
is something other than a
IntegerRangesList
:
-
as(from, "IntegerRangesList")
: Whenfrom
is aIntegerRanges
, analogous toas.list
on a vector.
Arithmetic Operations
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.
Author(s)
M. Lawrence & H. Pagès
See Also
-
IRangesList objects.
-
IntegerRanges and IRanges objects.
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 <- 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