RleViewsList-class {IRanges} | R Documentation |
List of RleViews
Description
An extension of ViewsList that holds only RleViews objects. Useful for storing coverage vectors over a set of spaces (e.g. chromosomes), each of which requires a separate RleViews object.
Details
For more information on methods available for RleViewsList objects consult the man pages for ViewsList-class and view-summarization-methods.
Constructor
RleViewsList(..., rleList, rangesList)
:-
Either
...
or therleList
/rangesList
couplet provide the RleViews for the list. If...
is provided, each of these arguments must be RleViews objects. Alternatively,rleList
andrangesList
accept Rle and IntegerRanges objects respectively that are meshed together for form the RleViewsList. Views(subject, start=NULL, end=NULL, width=NULL, names=NULL)
:-
Same as
RleViewsList(rleList = subject, rangesList = start)
.
Coercion
In the code snippet below, from
is an RleViewsList object:
as(from, "IRangesList")
:Creates an
IRangesList
object containing the view locations infrom
.
Author(s)
P. Aboyoun
See Also
ViewsList-class, view-summarization-methods
Examples
## Rle objects
subject1 <- Rle(c(3L,2L,18L,0L), c(3,2,1,5))
set.seed(0)
subject2 <- Rle(c(0L,5L,2L,0L,3L), c(8,5,2,7,4))
## Views
rleViews1 <- Views(subject1, 3:0, 5:8)
rleViews2 <- Views(subject2, subject2 > 0)
## RleList and IntegerRangesList objects
rleList <- RleList(subject1, subject2)
rangesList <- IRangesList(IRanges(3:0, 5:8), IRanges(subject2 > 0))
## methods for construction
method1 <- RleViewsList(rleViews1, rleViews2)
method2 <- RleViewsList(rleList = rleList, rangesList = rangesList)
identical(method1, method2)
## calculation over the views
viewSums(method1)