Removes redundant SNPs based on the criterion of squared correlation (\(r^2\))
exceeding a specified threshold. Traverses SNPs in order and drops any
following SNPs that are redundant with a retained one.
Arguments
- R
Numeric matrix. LD correlation matrix.
- thresh
Numeric. Squared correlation threshold (e.g., 0.2). SNPs with
\(r^2 > thresh\) compared to a retained SNP are eliminated.
Value
Logical vector of length nrow(R); retained SNPs are indicated by TRUE.