[Bioc-devel] GenomicRanges::findOverlaps() ignoring chromosome information?

[Kevin Rue-Albrecht]

Dear maintainer, Dear all,

*Situation*
I have used the findOverlaps(function) to annotate differentially
methylated regions (DRMs) obtained using the bsseq Bioconductor package in
the *Bos taurus* genome. (No, you won't steal my experimental design :-P ).
I used the genome UMD3.1.75 as a reference for my analysis.

*Problem*
The genes found to overlap the DMRs genomic ranges are often on a different
chromosone than the DMR, although the start and end coordinate of DMRs and
gene do overlap in all cases.
This leads me to believe that the chromosome information is ignored in
findOverlaps(). Is this the case, or am I using the function incorrectly?
Note that it does happen that a "true hit" is returned, i.e. the
overlapping gene is present on the same chromosome, with start and end
overlapping the coordinates of the DMR.


*Attached for your use/testing:*

   - dmrs variable
   - script used to annotate dmrs with information about overlapping gene
      - Note that I have tried to set select to arbitrary, first and last
      with always the same issue. I would prefer to get a single hit at this
      stage rather than filter afterwards, but the latter remain a possible
      option if necessary.


Any help / solution / feedback welcome !

Best regards,
Kevin

-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en