feat(qtls): flagging trans QTL credible sets #973
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This PR depends on merging #946 |
…//github.com/opentargets/gentropy into 3718-flag-trans-qtls-in-credible-set-dataset
DSuveges
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DSuveges
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vivienho
reviewed
Jan 23, 2025
src/gentropy/dataset/study_locus.py
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| .groupby("studyLocusId") | ||
| .agg( | ||
| # If any of the tags of a locus is in trans position, the QTL is considered trans: | ||
| f.array_contains(f.collect_set("isTagTrans"), True).alias("isTransQtl") |
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Here it states that the QTL is considered trans if at least one tag is trans, but in the PR description it's mentioned that a QTL is considered trans when all tagging variants are trans?
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Yes, thank you for finding this discrepancy. I have changed my mind, but haven't updated the description.
vivienho
reviewed
Jan 23, 2025
| _df=( | ||
| spark.createDataFrame(self.GENE_DATA, self.GENE_COLUMNS).select( | ||
| f.struct( | ||
| "strand", |
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The first strand seems redundant
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Oh, yes, you are totally right.
vivienho
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Jan 23, 2025
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@vivienho thank you for reviewing the PR! I have addressed both comments. If the tests are all passing, I'll merge the branch. |
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✨ Context
QTL credible stets can be in trans or in cis position respective to the relative location of the measured gene. A QTL credible set is considered trans if:
A newly introduced boolean column is added to studyLocus schema. This column is nulls for credible sets of gwas (non-qtl) studies.