RleViewsList-class {IRanges} | R Documentation |
An extension of RangesList
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. As a Sequence
, RleViewsList
may be
annotated with its universe identifier (e.g. a genome) in which all of its
spaces exist.
For more information on methods available for RleViewsList objects consult the man pages for RangesList and Views-utils.
RleViewsList(..., rleList, rangesList, universe = NULL)
:
Either ...
or the rleList
/rangesList
couplet
provide the RleViews for the list. If ...
is provided, each
of these arguments must be RleViews objects. Alternatively,
rleList
and rangesList
accept Rle and Ranges objects
respectively that are meshed together for form the RleViewsList.
The universe is specified by the universe
parameter, which
should be a single string or NULL, to leave unspecified.
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL)
:
Same as RleViewsList(rleList = subject, rangesList = start)
.
In the code snippets below, from
is an RleViewsList object:
as(from, "IRangesList")
: Creates a CompressedIRangesList
object containing the view locations in from
.
as(from, "CompressedIRangesList")
: Creates a
CompressedIRangesList
object containing the view locations in
from
.
as(from, "SimpleIRangesList")
: Creates a SimpleIRangesList
object containing the view locations in from
.
P. Aboyoun
## 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 RangesList 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)