Uses PLINK clumping method, where SNPs in LD within a particular window will be pruned. The SNP with the lowest p-value is retained.
clump_data( dat, clump_kb = 10000, clump_r2 = 0.001, clump_p1 = 1, clump_p2 = 1, pop = "EUR" )
Clumping window, default is
Clumping r2 cutoff. Note that this default value has recently changed from
Clumping sig level for index SNPs, default is
Clumping sig level for secondary SNPs, default is
Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR. 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers