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

[Kevin Rue-Albrecht]

Hi again,

Update on my issue, although I haven't found the source of the error yet..
I have correct overlaps in one scenario, but not in another.  This suggests
that the findOverlaps() command works as expected on my data, but in the
second scenario I don't see where the error is yet, let me explain:

   - When I use my function OverlapDmrs.Gene with argument only.hits=TRUE,
   all the hits make perfect sense
      - Full command: dmrs_gene = OverlapDmrs.Gene(dmrs=dmrs,
      gene_track=ensGene.asFeatures, only.hits=TRUE, prefix.chr=TRUE)
   - When I use my function OverlapDmrs.Gene with argument only.hits=FALSE,
   the correct DMRs are annotated with the right start and stop position, but
   with an incorrect chromosome value (strangest thing is that chromosone 30
   should not exist in *Bos taurus*, while some hits state this value in
   the chromosome column)
      - Full command: dmrs_gene.all = OverlapDmrs.Gene(dmrs=dmrs,
      gene_track=ensGene.asFeatures, only.hits=FALSE, prefix.chr=T)


...
Now that I wrote that "out loud", I just got an idea where to look for the
source of the problem. Apologies for the spam, but if I find the solution,
I'll definitely bring a conclusion to this thread.

Kevin






On 19 September 2014 10:12, Kevin Rue-Albrecht <kevin.rue at ucdconnect.ie>
wrote:

> 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
>



-- 
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

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