Hi Dario,
Thanks for providing the file.
The file has 55780092 records in it and yes it only contains primary
alignments so this is the best situation for the pairing algorithm.
Here are the timings I get for the readBamGappedAlignmentPairs()
function (renamed readGAlignmentPairsFromBam() in de
Dear all,
No problem from my side, I can adapt DEXSeq to those changes.
Best regards,
Alejandro Reyes
Mike, Alejandro,
I also wonder about getting rid of the 'exonID' metadata column. This
is redundant with 'exonic_part_number'. Do you have a preference for
keeping one or the other?
Valer
Fine by me.
I am currently rewriting parathyroidSE to benefit from this and the
summarizeOverlaps changes. The workflow is greatly simplified.
Mike
On Jul 31, 2013, at 7:04 PM, Valerie Obenchain wrote:
> Hi Nico,
>
> (Adding Mike and Alejandro.)
>
> Because disjointExons() came from DEXSeq
Mike, Alejandro,
I also wonder about getting rid of the 'exonID' metadata column. This is
redundant with 'exonic_part_number'. Do you have a preference for
keeping one or the other?
Valerie
On 07/31/2013 10:04 AM, Valerie Obenchain wrote:
Hi Nico,
(Adding Mike and Alejandro.)
Because dis
Hi Nico,
(Adding Mike and Alejandro.)
Because disjointExons() came from DEXSeq I wanted to preserve the
behavior for backwards compatibility and familiarity to DEXSeq users.
There are a couple of changes I'd like to make so disjointExons() is
consistent with the other extractors in GenomicFea
Right this is what I meant with the captureOutput() snippet. Perhaps the whole
reactive dispatch loop could be run to log instead of the clever force-
directed graph of closures updating that Joe showed off after presenting
Wednesday.
No good deed goes unpunished, and this suggests that loggin
I don't know how this actually works in practice. But conceptually, I think
of moving a slider in an Shiny app as possibly executing some R code. It
will be important for production quality code release that we are able to
test that this code works in a easy and portable way. I realize we may not
On Mon, Jul 29, 2013 at 4:46 PM, Dan Tenenbaum wrote:
> Hi Winston,
>
>
>
> On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang wrote:
> > Hi everyone -
> >
> > Great to hear from you all on your thoughts about Shiny. I've tried to
> > answer some of Dan's questions below...
> >
> >
> >>>
> >>> 1) Te
Hej Val, I believe that one is for you :-)
When using the aggregateGenes=TRUE parameter of the disjointExons function, the
gene names are separated by a "+" character. Is there a particular reason for
that? The reason I'm asking is that in the "transcripts" column the transcripts
ID are separat
