Add X_ref parameter: accept reference panel genotype matrix instead of LD#134
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xueweic wants to merge 2 commits intoStatFunGen:mainfrom
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Add X_ref parameter: accept reference panel genotype matrix instead of LD#134xueweic wants to merge 2 commits intoStatFunGen:mainfrom
xueweic wants to merge 2 commits intoStatFunGen:mainfrom
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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
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Add X_ref parameter: accept reference panel genotype matrix instead of LD
When the number of variants P is large, the P×P LD matrix may be too large to fit in memory. Users can now pass X_ref (N_ref × P reference panel) directly instead of precomputing LD = cor(X_ref). When N_ref < P, ColocBoost computes LD products on the fly via t(X_ref) %% (X_ref %% v) / (N_ref - 1), avoiding the P×P memory cost. When N_ref >= P, LD is precomputed internally.