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Removed three local helpers (corr_filter, check_remove_highcorr_snp, remove_highcorr_snp) and consume pecotmr equivalents instead: - ld_prune_by_correlation replaces corr_filter - enforce_design_full_rank replaces check_remove_highcorr_snp (exported, imported via @importFrom) - drop_collinear_columns replaces remove_highcorr_snp (unexported in pecotmr; bound via getFromNamespace in zzz.R) multicontext_ld_clumping rewritten as a thin orchestrator over pecotmr::ld_clump_by_score: chr/pos parsed once, per-tau clumping via -log10(p) scoring, final clump over the union scored by MAF. All bigsnpr/bigstatsr boilerplate (FBM wrapping, single-variant shortcut) now lives in pecotmr. Migrated the corresponding testthat coverage to pecotmr. Kept qQTLR integration tests that exercise enforce_design_full_rank via the imported symbol and the warning path. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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