Check discrepancy of the linkage equilibrium and test statistics
Usage
check_ld_disc(indices, z, Chi2_quantile = NULL, LDm, clump_r2)
Arguments
- indices
Variant indices.
- z
Test statistic.
- Chi2_quantile
Quantile for declaring a mismatch. The default is the median of a Chi-squared distribution with one degree of freedom.
- LDm
LD matrix.
- clump_r2
Clumping threshold for extremely highly correlated variants.
Value
List of indices within each LD clump, corrected for the LD discrepancy.