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Add Weidner aging clock (fixes #135) #184

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4983371
Upload Weidner CSV
alexiszxcv Mar 4, 2025
3db49a9
Update model definition with Weidner
alexiszxcv Mar 4, 2025
67d5e14
Add expected_model_outputs and fixed doi link
chancenlaw Apr 29, 2025
d526983
Add Weidner.csv to data folder
chancenlaw Apr 29, 2025
e3a4f9a
Fix Weidner csv file
chancenlaw May 6, 2025
eb2a7be
Fix formatting and CSV whitespace issues
marcbal77 Nov 16, 2025
8d2e315
Update Weidner expected test outputs with correct values
marcbal77 Nov 16, 2025
57af298
Fix Weidner coefficients to match published paper
marcbal77 Nov 18, 2025
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4 changes: 4 additions & 0 deletions biolearn/data/Weidner.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
CpGmarker,CoefficientTraining
cg02228185,-26.4
cg25809905,-23.7
cg17861230,164.7
12 changes: 12 additions & 0 deletions biolearn/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -641,6 +641,18 @@ def preprocess(df):
"file": "DepressionBarbu.csv",
},
},
"Weidner": {
"year": 2014,
"species": "Human",
"tissue": "Blood",
"source": "https://doi.org/10.1186/gb-2014-15-2-r24",
"output": "Age (Years)",
"model": {
"type": "LinearMethylationModel",
"file": "Weidner.csv",
"transform": lambda sum: sum + 38.0,
},
},
"TranscriptomicPredictionModel": {
"year": 2015,
"species": "Human",
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11 changes: 11 additions & 0 deletions biolearn/test/data/expected_model_outputs/Weidner.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
,Predicted
GSM1009660,21.621698419999998
GSM1009661,20.56664234
GSM1009662,19.783706960000004
GSM1009663,12.604693744999999
GSM1009664,25.795075009999994
GSM1009665,19.8254108
GSM1009666,18.693493688000004
GSM1009667,21.979727899999997
GSM1009668,14.975790068000002
GSM1009669,15.486470720000007