Perform conditional analysis using GCTA COJO

Source: R/cojo.r

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

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