Export af (not MAF) in top_loci; add medianAbsCorr; PIP screen after harmonization#530
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danielnachun merged 3 commits intoJun 23, 2026
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…harmonization top_loci now exports the effect-allele frequency as an af column instead of MAF, and the GwasSumStats/QtlSumStats methods actually wire the QC'd entry frequency into it (it was never passed before, so the old MAF column was always NA). af is the harmonized, complemented frequency; NA when absent. fineMappingPipeline gains a medianAbsCorr argument (default NULL), threaded to susie_get_cs for OR-logic credible-set purity alongside minAbsCorr. The optional PIP screen now runs after panel-vs-sumstats allele harmonization, so it operates on the harmonized variant set. Tests: update the MAF->af schema assertions and add coverage for af passthrough, medianAbsCorr OR-logic, and the PIP-screen ordering. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The CI's conda-forge susieR (CRAN build) has no median_abs_corr in susie_get_cs; guard the new OR-logic test so it runs only where susieR supports it (GitHub-HEAD) and skips otherwise. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Replace the hand-rolled fixed-ridge conditional with susieR's kriging RSS diagnostic: estimate the LD-mismatch scale via estimate_s_rss() and take the per-variant conditional distribution from kriging_rss(), flagging outliers on its standardized residual. krigingOutlierQc now takes n (threaded from the QC call site) and errors clearly when susieR lacks the diagnostic; ridge is gone. Better calibrated than the fixed ridge, which over-flagged in the tails (chr21 reference: 28 -> 8 flagged, the 8 a strict subset). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
top_lociexportsaf, notMAF.getTopLoci(posterior + marginal views) and the canonicalbuilder now emit an effect-allele-frequency
afcolumn. The GwasSumStats/QtlSumStats methods alsowire the QC'd entry frequency into it — it was never passed before, so the old
MAFcolumn wasalways
NA.afis the harmonized, complemented frequency;NAwhen absent.medianAbsCorris now afineMappingPipelineargument (defaultNULL), threaded tosusie_get_csfor OR-logic credible-set purity alongsideminAbsCorr.panel-aligned variant set.
No backward-compatibility shims (alpha).
Tests
Updated the
MAF→afschema assertions and added coverage for af passthrough (directional,NAwhen unsupplied),
medianAbsCorrOR-logic (admits ≥ sets;NULLno-op), and the PIP-screen ordering(an off-panel signal no longer rescues a region; screen-off is unchanged). Full affected suite green:
443 tests / 1125 expectations, 0 failures.