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feat(feature_matrix): extract features for gwas associations only #901

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merged 2 commits into from
Nov 5, 2024

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@ireneisdoomed ireneisdoomed commented Nov 5, 2024

✨ Context

This PR changes the LocusToGeneFeatureMatrixStep step to write only annotation for credible sets from GWAS. This is based on a conversation with @addramir, for now we are not planning to use this dataset for associations that don't have a L2G.

Dataset: gs://ot-team/irene/l2g/05112024/feature_matrix_filtered

The filter reduces the size of the dataset from 7Gb (103,256,085 rows) to 730Mb (18,991,756 rows). I haven't measured it, but the step is also significantly faster to generate.

The issue of the distance scores > 1 is also gone.

🛠 What does this PR implement

🙈 Missing

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  • Do these changes cover one single feature (one change at a time)?
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@ireneisdoomed ireneisdoomed merged commit 2af1074 into dev Nov 5, 2024
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@ireneisdoomed ireneisdoomed deleted the il-filter-fm branch November 5, 2024 14:18
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