bio-learn / bio-learn/biolearn

GrimAge not matching what I get from Clock Foundation

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#101 5 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
91
Forks
39
PR merge metrics
No merged PRs in 30d

Description

I've tried translating the model for GrimAge from python into R and calculating GrimAge on my own. I'm comparing it to GrimAge that I get from submitting the same data to the Clock Foundation online calculator. I'd love to be able to just use the code and not the black box that is the clock foundation website. Has anyone else tried this comparison? I'm wondering if the clock foundation provides values for CpGs that are missing from the dataset without telling you, but then I would expect every sample to be shifted equally in the same direction, if the same beta is being supplied to everyone. But my estimates and component scores are not shifted reliably like that. Thoughts?

Contributor guide

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Research direction

Start by locating the Python GrimAge model implementation and compare its inputs, missing-CpG handling, and component scores with the same data sent to the Clock Foundation online calculator. Reproduce the discrepancy across samples and document whether the implementation or input assumptions account for the differing GrimAge values.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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