[R] How to access values in s4 method

[David Winsemius]

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