RSS QC summary logging + fine-mapping vignette on current API#520
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Yining97 wants to merge 2 commits into
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RSS QC summary logging + fine-mapping vignette on current API#520Yining97 wants to merge 2 commits into
Yining97 wants to merge 2 commits into
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matchRefPanel exposes sign/strand-flip and drop counts via a qcCounts attribute; the summary-stats QC track now logs N-of-M per step (corrected vs removed vs imputed, kept distinct) and a per-study rollup. Migrate fine-mapping.Rmd to the camelCase API and finemappingOpts passthrough; top_loci schema maf -> af. Logging is observability only — QcResult and credible sets are unchanged (chr21 AD_Bellenguez: ΔPIP=0, identical CS). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Superseded by #522 |
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What
Two pecotmr-only follow-ups deferred by the earlier RSS steps.
Per-step QC summary logging. The summary-statistics QC track now reports how many
variants of how many each step touched, with the right verb per category:
kept N of M (corrected: sign-flipped A, strand-flipped B; dropped C)removed D of N(outliers dropped, never "flipped")before -> after (net +K)QC summary [study]: 9633 in -> 10184 out | corrected: sign-flip 0, strand-flip 0 | removed: harmonization 1 | imputed +552The counts already existed but were discarded:
matchRefPanelnow exposes them via aqcCountsattribute (default return shape unchanged, non-RSS callers unaffected),rssBasicQcthreads them through, and the orchestrator logs them.Fine-mapping vignette.
vignettes/fine-mapping.Rmdwas broken by the camelCaserefactor and the finemappingOpts/af changes. It now uses the current API (
ldData,zMismatchQc,finemappingMethod, fit params insidefinemappingOpts,top_loci.af)and knits end-to-end.
Guarantee
Logging is observability only. On chr21 AD_Bellenguez the QC result and credible sets
are byte-identical to the pre-logging code: variant set identical, max |ΔPIP| = 0,
CS membership identical, max |Δpurity| = 0.
Tests
matchRefPanelqcCounts test and QC-track message tests (N-of-M, rollup,skipped-step correctness, removed-not-flipped).
Out of scope (tracked in OpenSpec
xqtl-protocol-rss-api-sync): the xqtl-protocolnotebook migration and SoS end-to-end parity. A CI/pixi susieR bump to exercise
median_abs_corr end-to-end is flagged for later.