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?
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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
Hi Fahim, On Thu, Oct 21, 2010 at 2:05 PM, Fahim Md <fahim.md at gmail.com> 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??A few things: (1) You generally shouldn't cross post between two lists (2) This is more of a bioconductor question, so if you want further help, switch over to the bioc mailing list. (3) Read through the help in ?findOverlaps and pay attention to the links in the "See Also" section, which will take you to the "RangesMatching" class -- which is the result of a findOverlaps call (in case you were wondering how David was able to figure out how to point you to the ?"RangesMatching-class" help). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact