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feat(l2g): limit l2g predictions to gwas-derived associations #408

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merged 3 commits into from
Jan 12, 2024

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ireneisdoomed
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... as discussed with @d0choa and @addramir

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codecov-commenter commented Jan 12, 2024

Codecov Report

Attention: 129 lines in your changes are missing coverage. Please review.

Comparison is base (42b366c) 85.67% compared to head (bdcb218) 86.20%.
Report is 54 commits behind head on dev.

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@@            Coverage Diff             @@
##              dev     #408      +/-   ##
==========================================
+ Coverage   85.67%   86.20%   +0.53%     
==========================================
  Files          89       95       +6     
  Lines        2101     2596     +495     
==========================================
+ Hits         1800     2238     +438     
- Misses        301      358      +57     
Files Coverage Δ
src/airflow/dags/common_airflow.py 90.38% <100.00%> (ø)
src/airflow/dags/dag_preprocess.py 100.00% <ø> (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/cli.py 91.66% <100.00%> (+21.66%) ⬆️
src/otg/common/session.py 87.50% <100.00%> (+0.32%) ⬆️
src/otg/config.py 100.00% <100.00%> (ø)
src/otg/dataset/dataset.py 91.80% <100.00%> (ø)
src/otg/dataset/l2g_feature_matrix.py 82.92% <100.00%> (+7.31%) ⬆️
... and 35 more

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@d0choa d0choa left a comment

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Sounds good. Look at the comment for a potentially useful refactor

@@ -62,9 +62,17 @@ def from_credible_set(
Returns:
L2GPrediction: L2G dataset
"""
gwas_study_locus = StudyLocus(
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this could be a reasonable StudyLocus method. Most likely we will use it again study_locus.filterByStudyType(study_index, ["gwas"]).

It's a refactor so it could go in a different PR

@ireneisdoomed ireneisdoomed merged commit 4eafaf2 into dev Jan 12, 2024
3 checks passed
@DSuveges DSuveges deleted the il-l2g-predictions branch January 17, 2024 13:04
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3 participants