RSS QC update: mafCutoff, AF complement on swap, kriging, qcMethod -> zMismatchQc#516
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… zMismatchQc Brings the RSS summary-stats path up to the QC controls the individual path already has, on top of the camelCase refactor (StatFunGen#514). - rssAnalysisPipeline() gains mafCutoff, filtering on the AF-derived MAF after harmonization and LD alignment. af drives the MAF; a missing af skips the filter with a warning. maf stays internal and is never exported. - matchRefPanel() gains colToComplement, which complements af (1-af) on allele swaps. The default is unchanged so non-RSS callers are untouched. - New opt-in krigingOutlierQc() LD-consistency prefilter (alleleFlipKriging, off by default). - qcMethod renamed to zMismatchQc across rssAnalysisPipeline, summaryStatsQc, the colocboost entry points, colocWrapper, and the twas sumstat pipelines. No alias (alpha phase); default none. - Fixes one call site StatFunGen#514 left on the removed snake summary_stats_qc (twasMultivariateWeightsSumstatPipeline). Tested against the modified package with susieR 0.16.4: 3072 pass, 0 fail. On chr21 AD_Bellenguez the behavior-preserving config reproduces the step-1 credible sets exactly (max abs PIP diff 0) and matches a manual susie_rss run. xqtl-protocol notebooks still pass qcMethod and need a follow-up to adopt zMismatchQc. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Step 2 of the RSS-parity plan, rebased onto the camelCase refactor (#514). Brings the RSS summary-stats path up to the controls the individual-level path already has.
What changes
rssAnalysisPipeline(): filters on the AF-derived MAF (min(af, 1-af)) after harmonization and LD alignment. af drives the MAF; a missing af skips the filter with a warning. maf stays internal, never exported.matchRefPanel(): complements af (1-af) on allele swaps, independent of the beta/z sign-flip path. Default unchanged, so MR/TWAS/mash callers are unaffected.alleleFlipKriging(off by default).none) acrossrssAnalysisPipeline,summaryStatsQc, the three colocboost entry points,colocWrapper, and both twas sumstat pipelines.summary_stats_qc(twasMultivariateWeightsSumstatPipeline).Testing
Run against the modified package with susieR 0.16.4. Full testthat suite: 3072 pass, 0 fail, 22 skip. On chr21 AD_Bellenguez the behavior-preserving config (
zMismatchQc='none', maf/kriging off) reproduces the step-1 credible sets exactly (max abs PIP diff 0), matches a manualsusie_rss()run, and recovers the 2nd credible set at low min_abs_corr against the previous run.Follow-up
xqtl-protocol notebooks (
rss_analysis.ipynb,colocboost.ipynb) still passqcMethodand need to adoptzMismatchQc; that protocol change is out of scope here.