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Perform LD Clumping Locally or via Reference Panel

clump_data_local.Rd

This function performs LD clumping using either a local PLINK binary file (bfile) or a 1000 Genomes super population panel. Requires the ieugwasr and plinkbinr packages.

Usage

clump_data_local(
  dat,
  pop = NULL,
  bfile = NULL,
  clump_kb = 10000,
  clump_r2 = 0.001,
  plink_bin = plinkbinr::get_plink_exe()
)

Arguments

dat

Data frame with columns SNP, pval.exposure; optional id.exposure.

pop

1000G super-pop for online clumping (AFR/AMR/EAS/EUR/SAS). Used when bfile is NULL.

bfile

PLINK reference panel prefix for local clumping (without .bed/.bim/.fam). If set, pop is ignored.

clump_kb

Window size in kb. Default 10000.

clump_r2

r^2 threshold. Default 0.001.

Path to PLINK executable (auto-detect via plinkbinr if NULL and bfile is set).

Examples

if (FALSE) { # \dontrun{
# Reference:
# - https://github.com/MRCIEU/TwoSampleMR/issues/173
# - https://blog.csdn.net/xiaozheng1213/article/details/126269969
library(ieugwasr)
library(plinkbinr) # devtools::install_github("explodecomputer/plinkbinr")
plinkbinr::get_plink_exe()

# Note: after using this, please check `leo_clump` column to see if they are all TRUE
# If it's contains F, it means no SNPs remained after clumping or something bad happened
} # }