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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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Multi-ancestry analysis #27

Open kruthikaiyer0990 opened 2 months ago

kruthikaiyer0990 commented 2 months ago

Hi, Thank you for creating this software. In the paper (https://www.nature.com/articles/s41467-021-22334-6), it was noted that LOGODetect was utilized for a single-population-cross trait analysis involving 7 neuropsychiatric traits. The GitHub repository also provides an example of how to execute the algorithm for a cross-population analysis for one trait with EUR and EAS populations. Is it possible to extend this cross-population analysis to more than two populations? I attempted to include additional ancestry groups; no errors were thrown, but through the output I realized the algorithm only reads in the first two summary statistics and ignores the summary stats provided for other populations

Thanks, Kruthika

ghm17 commented 1 month ago

Hi Kruthika,

Thanks for using our tool! LOGODetect is designed to analyze two traits because (local or global) genetic correlation is defined over two traits. However, one can still anlayze more than two traits by doing a pairwise comparison, as we did in the paper. If a region is identified in multiple trait-pair analysis, then we can say that region is genetically associated with the traits involved in the trait-pairs. Hope this helps!

Best, Hanmin

kruthikaiyer0990 commented 1 month ago

Hi Hanim,

Thank you so much for your response. I was curious to understand if can we use LOGODetect to analyze one trait across more than 2 population ? I attempted to include 4 different ancestral groups but supplying summary stats for each of them; no errors were thrown, but through the output I realized the algorithm only reads in the first two summary statistics and ignores the summary stats provided for other populations. So is there a way that this can be done?

Best, Kruthika

ghm17 commented 1 month ago

Hi Kruthika,

LOGODetect currently can analyze one trait between 2 populations on each run. For analysis across more than 2 populations, say 4 in your case, you can supply 2 of 4 populations to LOGODetect each time and do 6 population-pairs in a parallel way. We will also update the software in the future, to incorporate the function that allows more than 2 traits/populations in a single run.

Best, Hanmin