Perform LD clumping on SNP data — clump

Uses PLINK clumping method, where SNPs in LD within a particular window will be pruned. The SNP with the lowest p-value is retained.

Usage

clump_data(
  dat,
  clump_kb = 10000,
  clump_r2 = 0.001,
  clump_p1 = 1,
  clump_p2 = 1,
  pop = "EUR",
  bfile = NULL,
  plink_bin = NULL
)

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 version of the EUR panel with a slightly different set of markers
bfile: If this is provided then will use the API. Default = NULL
plink_bin: If NULL and bfile is not NULL then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

Value

Data frame

Details

This function interacts with the OpenGWAS API, which houses LD reference panels for the 5 super-populations in the 1000 genomes reference panel. It includes only bi-allelic SNPs with MAF > 0.01, so it's quite possible that a variant you want to include in the clumping process will be absent. If it is absent, it will be automatically excluded from the results.

You can check if your variants are present in the LD reference panel using ieugwasr::ld_reflookup().

This function does put load on the OpenGWAS servers, which makes life more difficult for other users. We have implemented a method and made available the LD reference panels to perform clumping locally, see ieugwasr::ld_clump() and related vignettes for details.