clump: Perform LD clumping

In YangLabHKUST/MR-APSS: The MRAPSS package implement the MR-APPSS approach to test for the causal effect of an exposure on a outcome disease.

Perform LD clumping

Description

Peform LD clumping, to prune SNPs in LD within a window. Keep the most significant ones.

Usage

clump(
  dat,
  IV.Threshold = 5e-05,
  SNP_col = "SNP",
  pval_col = "pval.exp",
  clump_kb = 1000,
  clump_r2 = 0.001,
  clump_p = 0.999,
  pop = "EUR",
  bfile = NULL,
  plink_bin = NULL
)

Arguments

dat	a data frame must have columns with information about SNPs and p values
SNP_col	column with SNP rsid. The default is '"SNP"'
pval_col	column with p value. The default is '"pval"'
clump_kb	clumping window in kb. Default is 1000.
clump_r2	clumping r2 threshold. Default is 0.001.
clump_p	clumping significance level for index variants. Default = 5e-05
bfile	bfile as LD reference panel. If this is provided, then will use local PLINK. Default = NULL.
plink_bin	path to local plink binary. Default = NULL.

Value

data frame of clumped SNPs

YangLabHKUST/MR-APSS documentation built on April 13, 2025, 7:56 p.m.