Important update in Apr 2026#134
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xueweic merged 17 commits intoStatFunGen:mainfrom Apr 22, 2026
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Modify Code Only: Add X_ref parameter: accept reference panel genotype matrix instead of LD
Add unit test for the new implementation of X_ref
1. add use_entropy for leveraging trait heterogeneity when integrating weights 2. remove the dependency parameter from residual_correlation
add the consideration of the residual correlation
xueweic
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Add
X_refparameter and integration improvements1. New feature:
X_ref— memory-efficient LD handlingWhen the number of variants (P) is large, storing the full P × P LD matrix can exceed available memory. Users can now provide a reference panel genotype matrix (
X_ref, dimension N_ref × P) directly, and ColocBoost will compute LD products on the fly without materializing the full correlation matrix. Existing workflows using precomputed LD matrices are fully backward-compatible and require no changes.2. Entropy-based weight integration (optional)
Introduced two new optional parameters —
use_entropyandresidual_correlation— that allow users to incorporate trait heterogeneity when integrating evidence weights across outcomes. Both default toFALSE/NULLand do not alter existing behavior. Additionally, removed the legacydependencyadjustment from the variant selection step.3. Bug fixes
get_robust_colocalizationthat could produce incorrect results under certain input configurations.