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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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f2 from qpgraph with NULL as outgroup #44

Open ChiChunLiu opened 6 years ago

ChiChunLiu commented 6 years ago

Hi All,

I'm wondering what is the scale of f2 in qpgraph output? I set outgroup as NULL to turn off normalization but the resulting f2 seems to be normalized by heterozygosity somewhere. I tried to compute f2 and Fst myself, and my Fst agrees with qpgraph but f2 doens't.

I'm very grateful for the help.

Chi-Chun

bumblenick commented 6 years ago

We compute fst and f2 (unscaled) + std. error of fst call it fstsig a = fst/fstsig b = f2/fstsig (as vectors, division coefficient byy coefficient)

scale = a.b/b.b a least squares of b on a. The idea is to make f2 roughly comparable in size to fst.

Note that the scale factor is published in stdout and you can set a scale factor yourself overriding the default by lambdascale: in the parameter file.

Nick

On Wed, Oct 24, 2018 at 3:26 PM, Chi-Chun Liu notifications@github.com wrote:

Hi All,

I'm wondering what is the scale of f2 in qpgraph output? I set outgroup as NULL to turn off normalization but the resulting f2 seems to be normalized by heterozygosity somewhere. I tried to compute f2 and Fst myself, and my Fst agrees with qpgraph but f2 doens't.

I'm very grateful for the help.

Chi-Chun

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