[Bioc-sig-seq] countOverlaps With GRangesList

[Dario Strbenac]

Hello,

I have a group of genomic windows as a GRanges object, and a GRangesList object of length 6 (6 lanes of sequencing).

I think it should be possible to do counting of reads simply using countOverlaps :

> showMethods(countOverlaps)
...          ...          ...
query="GenomicRanges", subject="GRangesList"
...          ...          ...

But I only get one set of counts, not a matrix of 6 columns of counts.

> summary(aG)
 Length   Class    Mode 
  24966 GRanges      S4 
> summary(ipsList)
     Length       Class        Mode 
          6 GRangesList          S4
> str(countOverlaps(aG, ipsList))
 int [1:24966] 6 6 6 6 6 6 4 5 6 6 ...

Could this be a bug then ? Or is the design of the function intended for something different ?

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.2.3 IRanges_1.8.9      

loaded via a namespace (and not attached):
[1] tools_2.12.0

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia