Date: Wed, 11 May 2011 10:04:26 -0700
From: Marc Carlson <mcarlson at fhcrc.org>
Subject: Re: GenomicFeatures Introns
To: D.Strbenac at garvan.org.au
Hi Dario,
That is an interesting question with an interesting answer which I will
attempt to describe.
Our reasoning was that since introns are basically defined as the gaps
between exons within a transcript, we were not sure whether it would
ever really make sense to group them in another way. Basically I can
easily imagine why someone would want to count all the exons for a gene
or even why they might reduce something like that and then infer the
resulting gaps as universally intronic sequence (for that gene). But
that set of operations is NOT the same thing you would get if you
counted starting with a potential intronsBy() method. In fact, if you
had started with a naive intronsBy() method you might have horribly
miscounted since you would have all sorts of exonic regions contained in
some of your introns... :(
But perhaps you have another idea of how to sort this out? If you have
a compelling use case (and a way to do it that makes sense), please tell
us about it on the biod-devel mailing list.
Marc
On 05/11/2011 04:00 AM, Dario Strbenac wrote:
Hello,
I have a short design question. In a wiki page
http://wiki.fhcrc.org/bioc/Annotation_Helpers_Spec
It has a intronsBy(txdb, by) function described, but in GenomicFeatures, there's a intronsByTranscript function. Is there a reason why the Wiki intronsBy options were dropped (which is more like how exonsBy currently works) ? I didn't ask on the list, in case there was an obvious reason.
- Dario.