Unify compact top-loci export and SuSiE-Inf as the option for univaraite pipeline#504
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This update adds two fine-mapping output improvements while preserving existing default behavior. First, univariate fine-mapping can now bypass SuSiE-inf initialization when ordinary SuSiE fitting is explicitly requested. The SuSiE-inf path remains the default for compatibility, and TWAS-weight generation continues to require the existing SuSiE-inf workflow. Second, SuSiE wrapper output now includes a unified top-loci export table alongside the existing wrapper-facing summaries. The export keeps posterior effect summaries separate from marginal association fields, preserves credible-set membership including overlapping credible sets, and leaves existing top_loci and top_loci_long contracts unchanged. Focused regression tests cover the direct SuSiE path and the unified top-loci export contract.
Unify compact top-loci export at one wrapper boundary Major: - build_top_loci_long now emits the full annotated long: posterior conditional_effect / conditional_effect_se, cs_purity, per-fit n / variant_number / gene_id, and caller-supplied region / event_ID. - Adds build_top_loci_export(long): pure projection of the annotated long to the fixed 21-column compact export schema; stops on missing required columns rather than silently filling NA. Minor: - build_top_loci_long gains 3 default-NULL params (data_x, data_y, other_quantities); existing callers omitting them are unchanged. - .postprocess_finemapping_fit_common passes those through unchanged. - other_quantities reserves two subfield names for the unified export: region, condition_id (alongside the existing dropped_samples use). - .empty_top_loci_long extended with the new columns so empty and populated long share one schema. - Adds focused unit tests covering the new columns, the per-fit constants, the export helper schema, and the missing-column error. Loader, univariate_analysis_pipeline, and format_finemapping_output are unchanged. transMap-side adoption is out of scope of this commit.
gaow
reviewed
May 30, 2026
| coverage = c(0.95, 0.7, 0.5), | ||
| min_abs_corr = 0.8, | ||
| finemapping_extra_opts = list(refine = TRUE), | ||
| fit_susie_inf = TRUE, |
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could you change this to add_susie_inf otherwise users might think we can only fit one model at a time not another.
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Unify SuSiE top-loci output: one helper, one table
Major
build_top_loci_long/_wide/_exporttrio with singlebuild_top_loci()returning one 22-column table.postprocess_finemapping_fits()runs one method for-loop and rbinds per-method rows;format_finemapping_output()exposes onlytop_loci.Minor
build_top_loci()keeps the old long-builder input shape;data_x/data_y/other_quantitiesstay default-NULL.other_quantitiesreservesregionandcondition_id(alongsidedropped_samples).FineMappingResultS4 slot keeps legacy shape via back-compat alias insidesusie_wrapper.R;AllClasses.R/AllMethods.R/vcf_writer.Runchanged.<method>_<idx>CS strings,<method>_0PIP-only, per-method independent CS numbering,cs_95_purity = 0rule, overlapping CS within/across methods, singletop_locifield, removed-trio absence.Final
top_loci(22 cols)#chr,start,end,a1,a2,variantgene,eventn,maf,beta,sepip,posterior_effect_mean,posterior_effect_se,cs_95,cs_70,cs_50,cs_95_puritymethod,grange_start,grange_endConventions
cs_95/cs_70/cs_50are character"<method>_<idx>"(e.g."susie_1","susie_inf_2"); PIP-only retained variants use"<method>_0". Each method numbers CS independently from 1.cs_95_purity= 0.95-coverage purity for the row's(method, cs_95);"<method>_0"rows carry0.(variant, gene, method, cs_membership)— overlapping CS within a method and the same variant across methods both produce separate rows.SuSiE-Inf as the option for univaraite pipeline
Univariate fine-mapping can now bypass SuSiE-inf initialization when ordinary SuSiE fitting is explicitly requested. The SuSiE-inf path remains the default for compatibility, and TWAS-weight generation continues to require the existing SuSiE-inf workflow.