Move some qQTLR functions back to pecotmr for more general interests#472
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danielnachun merged 6 commits intomainfrom Apr 18, 2026
Merged
Move some qQTLR functions back to pecotmr for more general interests#472danielnachun merged 6 commits intomainfrom
danielnachun merged 6 commits intomainfrom
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Extracted from qQTLR's quantile_twas_weight.R to let qQTLR (and other downstream packages) consume these as library code instead of carrying their own copies. Four new helpers live in R/LD.R: - ld_prune_by_correlation (exported): hclust/cutree-based |cor| prune - enforce_design_full_rank (exported): QR-pivot iterative rank enforcement with a ld_prune_by_correlation fallback - drop_collinear_columns (internal): strategy-based single-column removal helper used by enforce_design_full_rank - ld_clump_by_score (exported): thin wrapper around bigsnpr::snp_clumping that handles FBM.code256 conversion and single-variant edge case All message() calls now gated behind verbose = FALSE (default silent). bigsnpr and bigstatsr added to Suggests; both use requireNamespace guards. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Small internal helper so pecotmr::twas_pipeline and qQTLR::quantile_twas_pipeline produce byte-identical per-(context, study) rows from twas_analysis() output. No new export, no NAMESPACE churn. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #472 +/- ##
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+ Coverage 27.48% 83.61% +56.12%
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Files 32 35 +3
Lines 4377 6682 +2305
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+ Hits 1203 5587 +4384
+ Misses 3174 1095 -2079 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Rename along the move to make it more informative.