runLDER: Main function

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

Main function

Description

Run LDER

Usage

runLDER(assoc, n.gwas, path, LD.insample = F, n.ld, ethnic = "eur",
  method = "lder", cores = 10, a = NULL, rough = T, twostage = T,
  type = "jack", n.bs = 1000)

Arguments

assoc	GWAS summary statistics, need to include snp, chr, a0, a1, z (header is necessary)
n.gwas	The sample size of the GWAS summary statistics
path	The output path
LD.insample	T/F, whether the LD reference is estimated with the GWAS cohort (T) or external reference panel (e.g. 1000 Genome Project) (F)
n.ld	The sample size of the LD reference
ethnic	Ethnic of the GWAS cohort; 'eur' for European ancestry
method	'lder', 'ldsc', or 'both'
cores	The number of cores for computation in parallel
a	Pre-specified inflation factor, default=NULL

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