Ranges object. As a Vector, RangesList may be
annotated with its universe identifier (e.g. a genome) in which all of its
spaces exist.
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.
universe identifier:
universe(x): gets the name of the universe as a
single string, if one has been specified, NULL otherwise.
universe(x) <- value: sets the name of the universe
to value, a single string or NULL.
RangesList(..., universe = NULL):
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. The universe is specified by the universe
parameter, which should be a single string or NULL, to leave unspecified.
x and from are 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).
as(from, "SimpleIRangesList"): Coerces from,
to a SimpleIRangesList, 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).
as(from, "CompressedIRangesList"): Coerces from,
to a CompressedIRangesList, 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).
as(from, "SimpleNormalIRangesList"): Coerces from,
to a SimpleNormalIRangesList, requiring
that all Ranges elements are coerced to internal
NormalIRanges elements.
as(from, "CompressedNormalIRangesList"): Coerces
from, to a CompressedNormalIRangesList,
requiring that all Ranges elements are coerced to internal
NormalIRanges elements.
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.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)
# set the universe
universe(named) <- "hg18"
universe(named)
RangesList(range1, range2, universe = "hg18")
## zoom in 2X
collection <- RangesList(one = range1, range2)
collection * 2
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