diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd index 8a616b6..ae67414 100644 --- a/vignettes/LD_Free_Colocalization.Rmd +++ b/vignettes/LD_Free_Colocalization.Rmd @@ -34,6 +34,7 @@ An inaccurate LD matrix may lead to unreliable colocalization results, especiall ### Why LD Mismatch Matters An inaccurate LD matrix can cause inconsistencies between the summary statistics and the reference LD matrix, leading to: + - Biased estimates of causal variants. - Increased computational time due to slower algorithm convergence. - Potentially misleading colocalization results. @@ -93,6 +94,7 @@ To address these challenges, ColocBoost provides two alternative approaches for with the assumption of one causal variant per trait per region: - **One iteration approach** (recommended): performing only 1 iteration of gradient boosting with the LD matrix ensures that: + - The LD matrix is only used to check the equivalence among trait-specific best update variants. - The accuracy of the results is improved compared to completely ignoring the LD matrix.