cojo_cond: Perform conditional analysis using GCTA COJO

In MRCIEU/gwasglue: GWAS summary data sources connected to analytical tools

Description

For a list of fine-mapped rsids, will assign to regions and generate conditionally independent summary stats for each rsid

Usage

cojo_cond(
  vcffile,
  bfile,
  snplist,
  pop,
  gcta = genetics.binaRies::get_gcta_binary(),
  workdir = tempdir(),
  threads = 1
)

Arguments

vcffile	Path to vcffile
bfile	LD reference panel
snplist	List of rsids
pop	EUR, ASN or AFR
gcta	Path to gcta binary. For convenience can use default=genetics.binaRies::get_gcta_binary()
workdir	Location to store temporary files. Default=tempdir()
threads	Number of parallel threads. Default=1

Value

List of independent summary stats

MRCIEU/gwasglue documentation built on Feb. 15, 2022, 3:25 p.m.