Hi Giovanni, two or three years ago I wrote an high performance extension module for finding associations between genetic markers in large population samples (in our case, about 50000 AIDS patients. Our markers were about 3000 SNPs). Its simple and fast: it can do the complete pairwise analysis to find markers with statistical association (3000 x 3000 markers in 50000 samples) in about a second on my laptop. The components that make this fast are mostly already in Pygr and I guess it would make sense to release the additional component (currently called snpindex) as part of Pygr. By the way, our data was more like haplotype data (i.e. each marker is either present vs. absent, instead of called as absent, heterozygous or homozygous as would be the case for a diploid genotype). So there isn't anything in this module that is specifically for genotype data.
I don't know if this is relevant to your interests. -- Chris Lee On Feb 17, 2009, at 5:40 AM, Giovanni Marco Dall'Olio wrote: > > Hi people, > I wonder whether pygr currently supports population genetics data and > if someone is using it in this field. > For example, how would I store a collection of genotypes in many > individuals, in pygr? > I must admit I haven't used pygr yet, and I wonder how it would be > difficult to write custom collection types or implement other > annations rather than sequences. > > Cheers :) --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
