Extract SNPs from vcf file

Source: R/proxy.r

Finds proxies if necessary

proxy_match(
  vcf,
  rsid,
  bfile = NULL,
  proxies = "yes",
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1,
  rsidx = NULL,
  dbfile = NULL
)

Arguments

vcf

vcf file name

rsid

list of rs IDs

bfile

ld reference panel (plink)

proxies

="yes" If SNPs are absent then look for proxies (yes) or not (no). Can also mask all target SNPs and only return proxies (only), for testing purposes

tag_kb

=5000 Proxy parameter

tag_nsnp

=5000 Proxy parameter

tag_r2

=0.6 Proxy parameter

threads

Number of threads to use (=1)

rsidx

Path to rsidx index

dbfile

ld tag database (sqlite)

Value

data frame