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
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 expla
Hi all, for this concluding email !
I found the problem in my code:
Everything was in the right place, except that I initialised the column
meant to store the chromosome name with NA values (DMRs without hits will
be left with this NA if the users requires all DMRs in the return value).
When I sub
Hi guys,
This is the problem of mapping back and forth between coordinate spaces,
such as between genomic and transcript space. I think there was some
progress this release cycle (introduction of mapCoords generic, etc), but I
think there is yet more to do. For example, transcriptLocs2RefLocs coul
On 19 September 2014 18:07, Michael Lawrence wrote:
> Hi guys,
>
> This is the problem of mapping back and forth between coordinate spaces,
> such as between genomic and transcript space. I think there was some
> progress this release cycle (introduction of mapCoords generic, etc), but I
> think
Hi,
It's an interesting problem. Right now mapCoords() has some
limitations. For example I can use it to map from reference sequence
to read cycle but not the other way around. Or from reference genome
to transcriptome but not the other way around (this reverse mapping
is actually what low level
Just a note to say thanks to those who worked on (1) the new biocViews
search capabilities and (2) seqlevelsStyle<-. These are great
improvements that have made tasks easier / faster time and time again.
Yea!
Val
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