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biostat0903 / DBSLMM

Deterministic Bayesian Sparse Linear Mixed Model
https://biostat0903.github.io/DBSLMM/
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Which column is the scaled effects, the third? the fourth? #23

Closed kkonoo closed 2 years ago

kkonoo commented 2 years ago

Hi, there! The third column of the output format is scaled effect sizes as written in your manual.rmd. image

However, according to your script, you seem to calculate PRS with the fourth column of DBSLMM output as follows. image

Which is correct?

biostat0903 commented 2 years ago

Hi, Sorry for the error. I update the manual in this page: https://github.com/biostat0903/DBSLMM. You can follow it. If there is any problem, you can ask me. Thanks for your attention to DBSLMM. Best, Sheng

kkonoo commented 2 years ago

Thank you for your fast reply. And I have another question. You say that the fourth column in the output file is non-scaled effect size. What does it mean? At first, I thought 'non-scaled' is the same with the effect size of the input summary file, but it was different from the ones in the input. How was the fourth column calculated?

Best, E.H.

biostat0903 commented 2 years ago

Hi, Thanks again for your attention to DBSLMM. Both third and fourth column is estimated from DBSLMM, that is, the effect size of mixed model. The third column is the scaled effect, and fourth column is non-scaled. We use MAF to transfer scaled size to non-scaled size. Best, Sheng

kkonoo commented 2 years ago

Oh, I see. Thank you for the reply!

Best, E.H.