feat: add the step class for fine-mapping #554
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| cred_set.tolist(), | ||
| ["variantId", "posteriorProbability", "logBF", "beta"], | ||
| ) | ||
| .join( |
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At this join the mode is inner by default. Is it expected?
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Yes, it should be 1 to 1 the same size and order
src/gentropy/susie_finemapper.py
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| session (Session): Spark session | ||
| _studyId (str): study ID | ||
| _region (str): region | ||
| _join (DataFrame): DataFrame with variant information |
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I would rename the _join variable to something more intuitive.
src/gentropy/susie_finemapper.py
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| order_creds.sort(key=lambda x: x[1], reverse=True) | ||
| cred_sets = None | ||
| counter = 0 | ||
| for i, value in order_creds: |
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i is fine, this is a scanonical way of calling an index variable, however value is not very telling. At row 110 it is very complicated what does this valuerefer to.
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renamed it for cs_lbf_value
| susie_output (dict[str, Any]): SuSiE-inf output dictionary | ||
| session (Session): Spark session | ||
| _studyId (str): study ID | ||
| _region (str): region |
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Do we have a consisted way of representing regions? If so, in the args description could be written eg.:
_region (str): finemapped region in chr:start-end format
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No, we don't have it now. But agree, we need to think about the standard.
src/gentropy/susie_finemapper.py
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| if cred_sets is None: | ||
| cred_sets = cred_set | ||
| else: | ||
| cred_sets = cred_sets.union(cred_set) |
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I would use unionByName rather union, because union concatenates columns by positions instead of names. I think in this case it is fine, as the order of columns are defined in rwo 120, but still.
| _join=gwas_df, | ||
| cs_lbf_thr=2, | ||
| ) | ||
| assert isinstance(L1, StudyLocus), "L1 is not an instance of StudyLocus" |
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I'm not sure how does the test dataset look like, it would be great to assert that the number of credible set is what you are expecting, and validate if the locus object is healthy. However I understand if that is not a high priority for now.
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I think we can create more meaningful test for bigger function that will use this convertor on later stages.
✨ Context
This PR introduced the fine-mapper step and has a function that converts susie output to study-locus.
🛠 What does this PR implement
See above.
🙈 Missing
Documentation will be updated later.
🚦 Before submitting
devbranch?make test)?poetry run pre-commit run --all-files)?