| RangesList-class {IRanges} | R Documentation |
An extension of AnnotatedList 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 an AnnotatedList, RangesList
may be annotated with its universe identifier (e.g. a
genome) in which all of its spaces exist.
In the code snippets below, x is a RangesList
object.
All of these accessors collapse over the spaces:
start(x): Get the starts of the ranges.end(x): Get the ends of the ranges.width(x): Get the widths of the ranges.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.
These accessors are for the 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.
In the code snippets below, x is a RangesList object.
x[i]: Subset x by index i, with the
same semantics as a basic TypedList, except
i may itself be a RangesList, in which case only the
ranges in x that overlap with those in i are kept. See
the overlap
method for more details.
In the code snippets below, x and from are a
RangesList object.
as.data.frame(x, row.names = NULL, optional = FALSE):
Coerces x to a data.frame. Essentially the same as
calling as.data.frame(unlist(x)).
as(from, "RangedData"): Coerces from to a
RangedData with zero columns and the same
ranges as in from.
as(from, "IRangesList"): Coerces from, to an
IRangesList, 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).
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
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 # subset by RangesList range1 <- IRanges(start=c(1,2,3), end=c(5,2,8)) range2 <- IRanges(start=c(1,15,20,45), end=c(5,15,100,80)) collection <- RangesList(one = range1, range2) collection[RangesList()] # empty elements collection[RangesList(IRanges(4, 6), IRanges(50, 70))] collection[RangesList(IRanges(50, 70), one=IRanges(4, 6))] # 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 * 2