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YangLabHKUST / MR-APSS

Mendelian Randomization accounting for Pleiotropy and Sample Structure using genome-wide summary statistics
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LD clumping for MR-APSS #2

Open xuj18 opened 11 months ago

xuj18 commented 11 months ago

Hi Yang Lab, I am trying to use MR-APSS for my analysis but I keep encountering a traffic issue for weeks for the LD clumping (see below) which severely impacts my use of MR-APSS. Is there any way you would recommend to overcome this issue? Thank you so much for your help!

Clumping h7AbIt, 440 variants, using EUR population reference Server code: 502; Server is possibly experiencing traffic, trying again... Server code: 502; Server is possibly experiencing traffic, trying again... Server code: 502; Server is possibly experiencing traffic, trying again... Server code: 502; Server is possibly experiencing traffic, trying again... Server code: 502; Server is possibly experiencing traffic, trying again... Server code: 502; Server is possibly experiencing traffic, trying again... Server error: 502 Failed to retrieve results from server. See error status message in the returned object and contact the developers if the problem persists.

Best, Jiayi

hxh0928 commented 1 month ago

The default setting for LD clumping is using the OpenGWAS API. Users do not need to specify the LD reference panel and the path to the plink binary. However, it may suffer from traffic issues when OpenGWAS servers are overloaded. To circumvent potential traffic issues, users can perform LD clumping locally by specifying the LD reference panel and the path to the plink binary using parameters "bfile" and "plink_bin".