Add Weidner aging clock (fixes #135)#184
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sarudak
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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)
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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 |
sarudak
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Let's just move forward with what we have since we don't have any stronger validation for this.
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)