Find LD proxies for a set of SNPs — get_ld_proxies • gwasvcf

Find LD proxies for a set of SNPs

get_ld_proxies(
  rsid,
  bfile,
  searchspace = NULL,
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1,
  out = tempfile()
)

Arguments

rsid: list of rs IDs
bfile: ld reference panel
searchspace: Optional list of rs IDs to use as potential proxies
tag_kb: =5000 Proxy parameter
tag_nsnp: =5000 Proxy parameter
tag_r2: =0.6 Proxy parameter
threads: Number of threads to use (=1)
out: temporary output file

Value

data frame