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wavelet screen + multi-region pipeline - #18
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Fix 1 (min_bins_per_ebnm_group): merge consecutive ebnm groups below a minimum bin count threshold in mf_prior_scale_mixture; prevents single-bin overfitting on coarse wavelet scales (lev 1 = 1 bin, lev 2 = 2 bins). Fix 2 (ebnm_null_prior_weight): pass optional prior_weights to ebnm_point_* to enforce a non-zero null component weight, analogous to mixture_null_weight on the mixsqp path. Fix 3 (cs_min_lead_pip): post-process the fit$sets$cs list to remove any credible set whose lead-SNP PIP falls below a threshold; targets diffuse extra CS formed by null effects in the per_scale_normal path. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
ebnm_point_normal has no prior_weights argument; the null weight constraint must be applied post-hoc by flooring fitted_g$pi[1] to ebnm_null_prior_weight and renormalizing slab weights. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
mf_low_count_indices was called after mf_quantile_normalize, so formerly-zero wavelet columns got median(|col|) ≈ 0.67 after qnorm and the threshold check (median ≤ 0) never fired. Near-zero-count modalities (e.g. Pois(0.001)) were unmasked → spurious log-BF → FDR inflation. Fix: compute lowc_idx on raw DWT output, then apply qnorm, then zero the flagged columns. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
When a subset of n samples from N3finemapping$X contains constant columns (xtx_diag_list[[m]] == 0), dividing XtR by zero produced NaN in bhat_m. This propagated through mf_em_likelihood_per_scale into colSums(abs(L)) == 0, which returned NA instead of TRUE/FALSE, causing 'missing value where TRUE/FALSE needed' in mf_em_m_step_per_scale. Fix: guard both mf_per_outcome_bhat_shat and refresh_iter_cache with a zero-pw mask that sets bhat=0 / shat=1 for constant predictors, matching the treatment already applied to low-count wavelet columns. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…esult Implements OpenSpec add-wavelet-pipeline-and-multiregion (meeting 2026-10-06). mfsusie_screen(): wavelet-level marginal association screen for a single region. Runs mf_dwt() + optional mf_quantile_normalize() per outcome, computes Pearson-correlation t-statistics over all (wavelet col x outcome x SNP) triples, returns min_pval and passed flag at configurable p_cutoff (default 1e-5). Scalar outcomes (T_m=1) are skipped. mfsusie_pipeline(): multi-region entry point. Accepts a list of regions (each with X, Y, pos, region_id), optionally screens with mfsusie_screen(), fits mfsusie() on passing regions, returns results + analysis funnel. Supports parallel execution via parallel::mclapply. Parameters: use_wavelet_filter, wavelet_qnorm, p_cutoff, n_cores, verbose. mfsusie_empty_result(): structured empty mfsusie object (class mfsusie/susie) returned for screen-rejected or fit-failed regions. Carries region_id, status, and min_pval in $screen_result. mfsusie_is_empty(): predicate used by predict/coef/fitted/print guards. Guards added to predict.mfsusie, coef.mfsusie, fitted.mfsusie, print.mfsusie so empty results do not error downstream. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- summary.mfsusie: add mfsusie_is_empty() guard (CONFIRMED: crashed on empty result) - mfsusie_screen: switch cor() to pairwise.complete.obs (PLAUSIBLE: listwise deletion shrank effective n across all pairs when any wavelet column had NAs) - mfsusie_pipeline: convert mclapply try-error returns to fit_failed empty results (PLAUSIBLE: OOM-killed workers returned try-error, not NULL, crashing the funnel-build loop) - tests: add summary() empty-result test; add mixed-pass/reject two-region pipeline test to cover funnel assembly and results list consistency (CONFIRMED: make_regions() was defined but never wired into a test block) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
fix: per_scale_normal FDR fixes, lowc_wc ordering, and zero-xtx guard
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