Export effect-allele af (not directionless maf) in top_loci (Step 1)#513
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- build_top_loci/.empty_top_loci + post-processing chain: column/arg maf -> af - susie_rss_pipeline forwards sumstats$af; univariate_analysis_pipeline gains optional directional af (exported; maf kept for filtering only) - load_rss_data: af declared only via explicit column-file mapping, with distinct one-time warnings; standardise_sumstats_columns shields explicit declarations so they win over MungeSumstats - misc::maf_from_af() helper; MAF is now internal/derived, never exported - tests: build_top_loci migration gate -> af; 6 load_rss_data af scenarios - man pages updated Verified on chr21:24215031-26405838 (AD_Bellenguez): credible sets / PIP / purity identical to the base run; only delta is maf -> af. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Jun 11, 2026
…finemapping_fits The maf->af rename in StatFunGen#513 missed multivariate_analysis_pipeline, which broke test_multivariate_pipeline.R. The multivariate maf is directionless and only used for filtering, so leave af unset (top_loci$af = NA) instead of relabeling it. Added a test. Pending follow-up: give multivariate_analysis_pipeline its own optional directional af input so it can export a real af, like univariate does.
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Step 1 of the RSS-parity plan: top_loci exports
af(effect-allele frequency,LD/reference-aligned) instead of directionless
maf; MAF becomes internal/derived.afpopulated only via an explicitaf:column-file declaration with a resolvableeffect allele (else NA + one warning); ambiguous FRQ/AF/allele_frequency/EAF never
become
af; explicit declarations win over MungeSumstats.chr21:24215031-26405838 (AD_Bellenguez, susieR 0.16.4) — credible sets / PIP identical
to the 5c729fa base (Jaccard 1.00, PIP corr 1.000); 2nd-CS / min_abs_corr behavior
unchanged. Only delta is the maf -> af column.
(a failing demonstration test is staged for that step).
🤖 Generated with Claude Code