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

avilella avilella at ebi.ac.uk
Mon Mar 1 07:53:55 EST 2004


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:


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

Any comments about the logic, naming, interest of this methods?



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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