[Bioperl-l] Getting IC & Consensus with
skirov at utk.edu
Mon Mar 14 09:47:21 EST 2005
Edward Wijaya wrote:
> Dear Stefan and James,
> Thanks so much for answering
> On Mon, 14 Mar 2005 21:15:43 +0800, Stefan Kirov <skirov at utk.edu> wrote:
>> The rules for too low are:
> Got it Stef.
>> I can fix this, but do you really want to get in your consensus a
>> position with proba less than 0.5?
> Yes, Don't you think by default it should be that way?
> Besides it'll be nice to have an *option* of how are we going to get
> the Consensus.
I'll commit the code tomorrow, just update your bioperl-live
>> We can easily add IC calculating method if you really need it.
> Yes, we definitely need that. I think naturally we would need the
> same as e-value.
You mean you want SiteMatrix to compute the e-value? Hmm... we are
getting out a bit out of scope here. Essentially PSM modules were
supposed only to provide data structure and parsers. And if IC is
generally straightforward and contained in the PFM/PSM, this is not the
case with e-val or p-val. Therefore I am reluctant to put it in PSM
> Actually I have the subroutine to compute the IC given the frequency
> You can use it to incorporate it to the module if you want, although
> it isn't a great piece of work.
> I just thought it may save you time.
Sure, that would be great. Just send it and I will optimize it if I can
and put it in. But maybe it should go to Bio::Tools... Any thoughts from
>> Please let me know if you have further questions.
> I'll save them till next time Stef ;-)
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