You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
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
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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: