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calculate a_hat, dispersion parameter #13

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GeorgeGkafas opened this issue Jul 8, 2024 · 0 comments
Open

calculate a_hat, dispersion parameter #13

GeorgeGkafas opened this issue Jul 8, 2024 · 0 comments

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@GeorgeGkafas
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Dear Xiao,

Thank you very much for developing Ballermix.
I used the b2 analysis per different Contigs of my data.
First I parse my VCF files using the default rec_rate and then following manual's steps I created the Site-Frequency-Specturm file.
The final script was the following

python BalLeRMix+_v1.py -i chr{i}_ballermix.txt --spect b2_spect-o chr{i}_B2scores.txt

I was wondering how I can calculate the a_hat dispersion parameter, as it's not present in the output file, or what I can tell about my results.
Here is a subset of my output file

genPos CLR x_hat s_hat A_hat nSites
0.0416375 3.4479299733187645 0.5 1000000000.0 10000 46
0.45881125000000006 6.3762486099960825e-06 0.4 1000000000.0 1000000.0 1
0.03548375 0.0 0.0 0.0 0.0 0.0
0.021341250000000003 0.002888251337004988 0.05 1000000.0 1000000.0 3
0.31978875 0.0 0.0 0.0 0.0 0.0
0.13466250000000002 3.356456799193211 0.5 1000000000.0 6000 71
0.37633000000000005 1.7426574919419409 0.5 100 4000 102

I understand that positive CLRs values are subject to balancing selection. But how can I tell if it's significant or not? Do you think a simple t-test, to test for significant non-zero values would answer my question?

Also, how can I interpret the selection coefficient's values?

Thanks
best,
George

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