[Biopython-dev] plink phasing and others

[Tiago Antão]

2012/4/16 Peter Cock <p.j.a.cock at googlemail.com>:
> Sounds good. The GO stuff would/should be more general than just
> PopGen, and I know other people are looking at this on branches.

What I do here is things like tree traversing (e.g. find all parent
nodes) and stuff like that. After that I do enrichment analysis
(fisher exact test, fdr, that stuff). Nothing of real interest for
now. I think we can ignore my code here (for now).

> When you said PCA, that was principle component analysis, right?

Yep, I am using eigenstrat/smartpca.

> What are you adding on top of NumPy/SciPy/matplotlib?

PCA plots and admixture plots.
Here is an example of both:
http://2.bp.blogspot.com/-6J6Gsas4uIs/TuELU3Gf4ZI/AAAAAAAAEWQ/CymvlzkX6hQ/s1600/PIIS0002929711004885.gr2_lrg.hi.jpg
TOP: PCA
Bottom: admixture



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"Liberty for wolves is death to the lambs" - Isaiah Berlin