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....@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel