-
Notifications
You must be signed in to change notification settings - Fork 33
Add Weidner aging clock (fixes #135) #184
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
base: master
Are you sure you want to change the base?
Conversation
sarudak
left a comment
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
The testset data was committed. Please remove and ensure that the large methylation file is cleaned out of the history.
Corrected coefficients from the original PR to match the published formula in Weidner et al. 2014 (doi: 10.1186/gb-2014-15-2-r24): - cg02228185: -26.4 (was -64.57) - cg25809905: -23.7 (was -42.57) - cg17861230: 164.7 (was 75.15) - Intercept: 38.0 (was 111.83)
|
Changes made:
The PR now only adds the 3 essential files (27 lines total) - the model definition, coefficients file, and expected test outputs. cc: @chancenlaw @alexiszxcv - I preserved your original work, just fixed the coefficients to match the paper and cleaned up per review feedback + @sarudak |
Adds the Weidner blood-based aging clock (2014) to biolearn, implementing the 3-CpG age prediction model. This supersedes #135 and addresses all review feedback.
The Weidner clock uses DNA methylation at 3 CpG sites (ASPA, ITGA2B, PDE4C) to predict age from blood samples with ~5 year accuracy. Reference: Weidner et al., 2014
Changes:
Addresses review concerns from #135:
Closes #135, closes #170
cc: @chancenlaw @alexiszxcv (original PR authors), @sarudak (reviewer)