On Oct 21, 2010, at 8:05 PM, Fahim Md wrote:
Hi
How to access the values in the output that is an object of S4 type.
I tried
to access using subset ( [ ] ) but it is not allowed.
Any clue??
Thanks
-- Fahim
#My code is as follows:
require(IRanges);
query <- IRanges(c(1, 4, 9), c(5, 7, 10))
subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
findOverlaps(query, subject)
Output of find overlap function is:
------------------
1> findOverlaps(query, tree)
An object of class "RangesMatching"
Slot "matchMatrix":
query subject
[1,] 1 1
[2,] 1 2
[3,] 3 2
Slot "DIM":
[1] 4 3
--------------------
How to access the values in the output?
> ?"RangesMatching-class" # to determine accessor functions
> ovrl <- findOverlaps(query, subject)
> as.table(ovrl)
[1] 2 0 1
> ? findOverlaps
> as.matrix(ovrl)
query subject
[1,] 1 1
[2,] 1 2
[3,] 3 3
> dim(ovrl)
[1] 3 3
--
David Winsemius, MD
West Hartford, CT
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