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ghm17 / LOGODetect

LOGODetect is a powerful tool to identify small segments that harbor local genetic correlation between two traits/diseases.
GNU General Public License v3.0
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What was the theta that produced the example output file? #8

Closed jdblischak closed 3 years ago

jdblischak commented 3 years ago

I finished the tutorial. The theta that was selected to produce the final output file was 0.65. However, the example results committed to the repo (#3) are much more similar to my results with theta 0.6. Could you please confirm which value of theta produced the results? I would like to know if I need to go back and double check how I ran the S-LDSC steps.

ghm17 commented 3 years ago

Your results are very similar but not identical to mine for both theta value 0.6 and 0.65. This is due to variation in random vector generation. In my implementation, I select the best theta 0.6 (proportion of genetic covariance = 11.63%), better than theta 0.65 (proportion of genetic covariance = 10.59%), but the difference is not substantial. You can check these values (/Temp/S-LDSC/LOGODetect_theta_0.6.log line 70) to confirm whether results are consistent.

jdblischak commented 3 years ago

Great! Thanks for the additional explanation. My results had a proportion of genetic covariance of 12.06% for theta=0.6 and 12.58% for theta=0.65. Below are the results for all values of theta:

% find output_dir/Temp/S-LDSC/ -regex '.*/LOGODetect_theta_0.[0-9]+.log' | sort | xargs -I {} bash -c "echo {}; head -n 70 {} | tail -n 1"
output_dir/Temp/S-LDSC/LOGODetect_theta_0.35.log
Proportion of gencov: 0.9124 0.0876
output_dir/Temp/S-LDSC/LOGODetect_theta_0.3.log
Proportion of gencov: 0.9202 0.0798
output_dir/Temp/S-LDSC/LOGODetect_theta_0.45.log
Proportion of gencov: 0.9046 0.0954
output_dir/Temp/S-LDSC/LOGODetect_theta_0.4.log
Proportion of gencov: 0.9124 0.0876
output_dir/Temp/S-LDSC/LOGODetect_theta_0.55.log
Proportion of gencov: 0.8906 0.1094
output_dir/Temp/S-LDSC/LOGODetect_theta_0.5.log
Proportion of gencov: 0.9021 0.0979
output_dir/Temp/S-LDSC/LOGODetect_theta_0.65.log
Proportion of gencov: 0.8742 0.1258
output_dir/Temp/S-LDSC/LOGODetect_theta_0.6.log
Proportion of gencov: 0.8794 0.1206
output_dir/Temp/S-LDSC/LOGODetect_theta_0.7.log
Proportion of gencov: 0.8801 0.1199