feat(coloc): single SNP case #511
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…tropy into coloc_unit_tests
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Added additional tests for other edge cases where the overlapping SNPs are not causal/ only causal in one study. The fix returns sensible results in both cases(high h0 or high h1). This doesn't happen in practice as we take the union of the overlaps between credible sets, in Finngen r10 for example there are 3.4k/39k studyLocusOverlaps which are single SNP, all of which are causal (min.PP = ~0.95, avg.PP=0.99). |
d0choa
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Mar 6, 2024
DSuveges
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Mar 8, 2024
* feat: include single snp overlaps in coloc calcs * chore: added unit test for coloc * feat: include single snp overlaps in coloc calcs * chore: added unit test for coloc * fix: check for differences in test results * fix: revert changes to single snp coloc tests for other pr * fix: revert single snp change * chore: restructure test folder * fix: compare differences in results rather than exact match * chore: test description * fix: allow for coloc when only one snp is overlapping * chore: include tests for h0 and h1/2 * fix: added pseudocount variable to coloc * fix: pseudocount as a Coloc attribute --------- Co-authored-by: David Ochoa <ochoa@ebi.ac.uk>
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no longer filtering out single snp studyLocusOverlaps.
when: f.col("sumlogsum") == f.col("logsum12") == 0 :
This causes problems when we have to log the result.
Instead of 0, replace with a very small number.
Works when one causal snp is overlapping, returns high h4 value very close to 1.