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"
)

Arguments

dat

Output from format_data. Must have a SNP name column (SNP), SNP chromosome column (chr_name), SNP position column (chrom_start). If id.exposure or pval.exposure not present they will be generated.

clump_kb

Clumping window, default is 10000.

clump_r2

Clumping r2 cutoff. Note that this default value has recently changed from 0.01 to 0.001.

clump_p1

Clumping sig level for index SNPs, default is 1.

clump_p2

Clumping sig level for secondary SNPs, default is 1.

pop

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

Value

Data frame