staar: heterogeneous MetaSTAAR, SCANG bridge + MC threshold#130
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staar: heterogeneous MetaSTAAR, SCANG bridge + MC threshold#130
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… threshold Three additions in one commit: Heterogeneous MetaSTAAR (#72) persists per-study U in the DuckDB merge via a new study_us column and adds MetaVariant.u_study so the conditional path at meta.rs:meta_score_gene_conditional can Schur- condition each study independently before summing the per-study (U_cond_i, K_cond_i). Mirrors MetaSTAAR R/MetaSTAAR_merge_cond.R:391- 404. The config rejection for --conditional-model heterogeneous is deleted. SCANG null-model bridge (#110) adds staar::scang::ScangExt on NullModel carrying pre-sampled pseudo-residuals from N(0, P) via projection sampling (no eigendecomp). Source: STAARpipeline R/staar2scang_nullmodel.R:23-34 for the unrelated gaussian path. Kinship and binary gates reject until the Cholesky factor bridge lands. SCANG MC empirical threshold (#79) wires the pseudo-residuals into the per-chromosome SCANG scoring at scoring.rs:compute_scang_threshold. For each window, per-sim burden U = G' z_j is scored against the cached K to produce a null distribution of max -log(p). The 1-alpha quantile (default alpha=0.05) floored at -log(1e-4) filters windows before emission. emthr column is written on every mask output parquet alongside STAAR-O.
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Heterogeneous MetaSTAAR (#72) persists per-study U via a new DataFusion study_us column in merge_chromosome and adds MetaVariant.u_study so the conditional scoring path can Schur-condition each study independently before summing. Mirrors MetaSTAAR R/MetaSTAAR_merge_cond.R:391-404. The heterogeneous reject at commands/meta_staar.rs is deleted.
SCANG bridge (#110) adds staar::scang::ScangExt on NullModel with pre-sampled pseudo-residuals from N(0, P) via projection sampling. Gaussian unrelated path only; kinship and binary gates reject until the Cholesky bridge lands. Source: STAARpipeline R/staar2scang_nullmodel.R:23-34.
SCANG MC threshold (#79) wires pseudo-residuals into per-chromosome SCANG scoring. For each window, per-sim burden statistic is scored against the cached K. The 1-alpha quantile of the resulting max-stat distribution, floored at -log10(1e-4), filters windows before emission. emthr column is written alongside STAAR-O on every mask output parquet. Source: SCANG R/SCANG.r:181-205.
Closes #72
Closes #110
Closes #79