generateLD: Calculate LD files

In shuangsong0110/LDER: Leveraging LD eigenvalue regression to improve the estimation of SNP heritability and confounding inflation

Calculate LD files

Description

Run LDER

Usage

generateLD(assoc, path, bfile_path, cores = 10, ethnic = "eur",
  plink_path = NULL, python_path = NULL)

Arguments

assoc	GWAS summary statistics, need to include snp, chr, a0, a1, z (header is necessary)
path	The output path
bfile_path	The path to the plink bfiles for LD estimation
cores	The number of cores for computation in parallel
ethnic	Ethnic of the GWAS cohort; 'eur' for European ancestry
plink_path	The path to the plink software. If not specified, the function will use the default path (which plink)
python_path	The path to the python software. If not specified, the function will use the default path (which python)

shuangsong0110/LDER documentation built on April 6, 2024, 4:17 a.m.