Interpretation of fastStructure chooseK.py output

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Rena Schweizer

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Apr 21, 2014, 3:54:03 PM4/21/14
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Hi,

I'm using fastStructure with a dataset of 123 individuals and ~24K LD-pruned SNPs. I ran fastStructure for K=1 to K=10 (the simple algorithm) and ran the chooseK.py script at the end. The output is:

Model complexity that maximizes marginal likelihood = 3
Model components used to explain structure in data = 5

When I look at the mean Q values for K=5 (e.g. output_simple.5.meanQ), it appears as though fastStructure was only able to assign 4 real groups meaning that all individuals have probability of assignment to only 4/5 groups. You can see this in the the meanQ file (at the end of this post).

Do you know why K=5 would be identified as best for explaining structure in the data in this case?

Thanks,
Rena


output_simple.5.meanQ:

0.000005 0.257709 0.000005 0.733769 0.008513
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999983 0.000004
0.000004 0.000004 0.000004 0.999980 0.000007
0.000004 0.000004 0.000004 0.818203 0.181784
0.000004 0.000004 0.000004 0.854659 0.145328
0.000004 0.000005 0.000004 0.999982 0.000004
0.000004 0.000004 0.000004 0.582430 0.417557
0.000004 0.000004 0.000004 0.419663 0.580324
0.000005 0.000005 0.000005 0.615712 0.384274
0.000004 0.000004 0.000004 0.442988 0.556999
0.000004 0.000004 0.000004 0.352215 0.647772
0.000004 0.000004 0.000004 0.406904 0.593083
0.000004 0.000005 0.000005 0.999982 0.000004
0.000004 0.000005 0.000004 0.965506 0.034481
0.000004 0.000005 0.000004 0.999356 0.000630
0.000004 0.000004 0.798158 0.201829 0.000004
0.000005 0.000006 0.000005 0.966547 0.033437
0.000004 0.000004 0.000004 0.711363 0.288624
0.000004 0.000005 0.000005 0.980660 0.019326
0.000004 0.000007 0.000004 0.991424 0.008561
0.000004 0.000004 0.000004 0.999979 0.000008
0.000004 0.000005 0.000004 0.999983 0.000004
0.000004 0.000005 0.000004 0.999983 0.000004
0.000004 0.999983 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999982 0.000005 0.000005 0.000005
0.000004 0.999983 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999983 0.000004 0.000004 0.000004
0.000005 0.000005 0.000005 0.999981 0.000005
0.000005 0.000005 0.000005 0.999980 0.000006
0.000004 0.000005 0.000004 0.999981 0.000005
0.000004 0.000005 0.000004 0.999981 0.000005
0.000004 0.999983 0.000004 0.000004 0.000004
0.000004 0.646696 0.000004 0.322599 0.030696
0.000004 0.999983 0.000004 0.000004 0.000004
0.000004 0.999982 0.000004 0.000004 0.000004
0.000004 0.999983 0.000004 0.000004 0.000004
0.000004 0.159721 0.000004 0.730277 0.109993
0.000004 0.030373 0.000004 0.920496 0.049123
0.000004 0.000004 0.000004 0.968637 0.031350
0.000004 0.000006 0.000005 0.950356 0.049629
0.000004 0.000004 0.000004 0.910326 0.089661
0.000004 0.000005 0.000004 0.999976 0.000010
0.000004 0.046454 0.000004 0.853010 0.100527
0.000004 0.000005 0.000004 0.966909 0.033078
0.000004 0.000005 0.000005 0.979361 0.020625
0.000004 0.000005 0.000004 0.932210 0.067776
0.000005 0.135089 0.000005 0.807125 0.057777
0.000004 0.000004 0.000004 0.950630 0.049357
0.000004 0.000004 0.999983 0.000004 0.000004
0.000004 0.000004 0.999983 0.000004 0.000004
0.000004 0.000004 0.999983 0.000004 0.000004
0.000004 0.000004 0.691252 0.308735 0.000004
0.000004 0.000004 0.000004 0.212793 0.787194
0.000004 0.000004 0.000004 0.202558 0.797429
0.000004 0.000004 0.000004 0.157692 0.842295
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000004 0.000004 0.000004 0.000004 0.999983
0.000005 0.000005 0.000005 0.000005 0.999982
0.000004 0.000004 0.000004 0.334066 0.665921
0.000004 0.000004 0.000004 0.328747 0.671241
0.000004 0.000004 0.000004 0.271564 0.728423
0.000004 0.000004 0.000004 0.318035 0.681952
0.000004 0.000004 0.000004 0.198410 0.801577
0.000004 0.000004 0.000004 0.600684 0.399303
0.000004 0.000004 0.000004 0.340345 0.659642
0.000004 0.000004 0.000004 0.303397 0.696590
0.000004 0.000004 0.000004 0.603612 0.396375
0.000005 0.000005 0.000005 0.381338 0.618648
0.000004 0.000004 0.000004 0.084648 0.915339
0.000004 0.000004 0.000004 0.972699 0.027288
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000005 0.000004 0.999982 0.000004
0.000004 0.000004 0.110335 0.889651 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999981 0.000005
0.000004 0.000004 0.000004 0.772947 0.227040
0.000004 0.000005 0.000004 0.998682 0.001305
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.108073 0.000004 0.761316 0.130603
0.000004 0.000004 0.000004 0.999982 0.000005
0.000005 0.000005 0.000005 0.999980 0.000005
0.000004 0.000005 0.000004 0.998788 0.001199
0.000004 0.000005 0.000005 0.999981 0.000006
0.000004 0.000004 0.000004 0.999980 0.000007
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000005 0.000004 0.999981 0.000006
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999983 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005
0.000004 0.000004 0.000004 0.999983 0.000005
0.000004 0.000004 0.000004 0.999982 0.000005

Vikram Chhatre

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Apr 21, 2014, 4:00:22 PM4/21/14
to structure-software
Rena -

The ChooseK utility gives you a range, not an optimal K value.  Based on the output from the script, the range of K values is between 3 and 5.

Also, you may want to plot membership coefficients for K3 through K5 and compare.

V



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