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chore(studylocus): rename logABF statistics to logBF #402

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merged 2 commits into from
Jan 11, 2024

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ireneisdoomed
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This PR includes:

  • Renaming of locus.logABF to locus.logBF in the StudyLocus schema. SuSiE outputs the statistical measure between a variant and a trait in the form of bayes factors. We used to capture the approximation of this value because of GCTA-COJO, our previous fine mapping algorithm.
  • Updates in the documentation and codebase

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Codecov Report

Attention: 91 lines in your changes are missing coverage. Please review.

Comparison is base (42b366c) 85.67% compared to head (9a8d64f) 85.84%.
Report is 48 commits behind head on dev.

Additional details and impacted files

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@@            Coverage Diff             @@
##              dev     #402      +/-   ##
==========================================
+ Coverage   85.67%   85.84%   +0.17%     
==========================================
  Files          89       96       +7     
  Lines        2101     2593     +492     
==========================================
+ Hits         1800     2226     +426     
- Misses        301      367      +66     
Files Coverage Δ
src/airflow/dags/common_airflow.py 90.38% <100.00%> (ø)
src/airflow/dags/finngen_preprocess.py 100.00% <100.00%> (ø)
src/airflow/dags/gwas_catalog_harmonisation.py 43.47% <ø> (ø)
src/airflow/dags/gwas_curation_update.py 100.00% <100.00%> (ø)
src/otg/common/session.py 87.50% <100.00%> (+0.32%) ⬆️
src/otg/dataset/dataset.py 91.80% <100.00%> (ø)
src/otg/dataset/l2g_feature_matrix.py 82.92% <ø> (+7.31%) ⬆️
src/otg/dataset/study_locus.py 96.20% <100.00%> (+0.04%) ⬆️
src/otg/datasource/finngen/study_index.py 100.00% <100.00%> (ø)
src/otg/datasource/finngen/summary_stats.py 100.00% <100.00%> (ø)
... and 24 more

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it's crazy the amount of changes required to rename a column in this case

@ireneisdoomed
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ireneisdoomed commented Jan 11, 2024

@d0choa In the schema, we could abstract the name of the statistic we use. Or capture both and just abstract COLOC. It is equally valid regardless of the fine mapping results you come with. But it's easier like this for now.
Thanks for the review!

@ireneisdoomed ireneisdoomed merged commit 7cb52bd into dev Jan 11, 2024
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@ireneisdoomed ireneisdoomed deleted the il-abf-schema branch January 11, 2024 09:21
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3 participants