Perform Clumping and Pruning
Usage
multicontext_ld_clumping(
X,
qr_results,
maf_list = NULL,
ld_clump_r2 = 0.2,
final_clump_r2 = 0.8
)
Arguments
- X
Matrix of genotypes
- qr_results
Results from QR_screen
- maf_list
List of minor allele frequencies (optional)
- ld_clump_r2
R-squared threshold for initial LD clumping based on pvalue
- final_clump_r2
R-squared threshold for final LD clumping based on MAF
Value
A list containing final SNPs and clumped SNPs