ld_local: clump function using local plink binary and ld reference...

In Osmahmoud/SlopeHunter: Slope-Hunter: A ROBUST METHOD FOR COLLIDER BIAS CORRECTION IN CONDITIONAL GENOME-WIDE ASSOCIATION STUDIES

clump function using local plink binary and ld reference dataset This function is modified from: https://github.com/MRCIEU/ieugwasr/blob/master/R/ld_clump.R

Description

clump function using local plink binary and ld reference dataset This function is modified from: https://github.com/MRCIEU/ieugwasr/blob/master/R/ld_clump.R

Usage

ld_local(dat, clump_kb = 250, clump_r2 = 0.1, clump_p1 = 1, bfile)

Arguments

dat	Dataframe. Must have a variant name column (rsid) and pval column called (pval).
clump_kb	Clumping window, default is 250.
clump_r2	Clumping r-squared threshold, default is 0.1.
clump_p1	Clumping sig level for index SNPs, default is 1.
bfile	Path to the bed/bim/fam LD reference (e.g. "1kg.v3/EUR" for local 1000 EUR ref. population file).

Osmahmoud/SlopeHunter documentation built on Oct. 7, 2022, 4:38 p.m.