Fwd: [Bioperl-l] Bio::PopGen::Statistics discrete calculations

[Matthew Hahn]

>----- Forwarded message from avilella <avilella at ebi.ac.uk> -----
>     Date: Mon, 01 Mar 2004 12:53:55 +0000
>     From: avilella <avilella at ebi.ac.uk>
>Reply-To: avilella <avilella at ebi.ac.uk>
>  Subject: [Bioperl-l] Bio::PopGen::Statistics discrete calculations
>       To: bioperl-ml <bioperl-l at bioperl.org>
>
>Hi,
>
>I'm interested in calculating some of the statistics in
>Bio::PopGen::Statistics in a discrete, position-wise, way.
>
>For example,
>
>I've done a quick implementation of the method "pi" that returns the
>value of the statistic for each polymorphic positions instead of the
>mean of all of them. It's "pi_discrete" method:
>
>http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-live/Bio/PopGen/Statistics.pm?rev=1.4&content-type=text/x-cvsweb-markup
>


Do you want to just calculate each site's heterozygosity?  Otherwise, 
I'm not quite sure what 'pi' means in this context.  The pi 
calculation currently implemented simply sums up each site's 
heterozygosity.





>I would also like to have methods to do Sliding Window calculations for
>these statistics. Something like:
>
>"Calculate tajima_D for windows of 100 polymorphisms that slide 10
>positions"
>
>Any comments about the logic, naming, interest of this methods?


Sounds great--I'm sure it would get used.  The only precaution I 
would give is that some of the formats for inputting the polymorphism 
data (i.e. prettybase files) do not have to include monomorphic 
sites.  This would really mess with any kind of sliding window.




cheers,
Matt



>Thanks,
>
>     Albert.
>
>--
>Albert Vilella Bertran    avilella_at_ebi_ac_uk
>EMBL Outstation, European Bioinformatics Institute
>Wellcome Trust Genome Campus, Hinxton
>Cambs. CB10 1SD, United Kingdom
>Phone: +44 (0)1223 494 448   FAX: +44 (0)1223 494 468
>
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>
>----- End forwarded message -----


-- 
Matthew W. Hahn
Center for Population Biology
2320 Storer Hall
University of California
Davis, CA 95616