RleViewsList-class {IRanges} | R Documentation |
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.
For more information on methods available for RleViewsList objects consult the man pages for ViewsList-class and view-summarization-methods.
RleViewsList(..., rleList, rangesList)
:
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.
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
ViewsList-class, view-summarization-methods
## 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)