Get proxies for variants from plink binary

Usage

get_proxies(
  x,
  stat = "r2-unphased",
  win_kb = 125,
  win_r2 = 0.8,
  win_ninter = Inf,
  proxy_eaf = NULL,
  plink2 = genepi.utils::which_plink2(),
  pfile = genepi.utils::which_1000G_reference(build = "GRCh37"),
  ...
)

Arguments

x: a character vector of rsids or a GWAS object
stat: character, the R stat to calculate, one of "r2-unphased", "r2-phased", "r-unphased", "r-phased"
win_kb: numeric, the window to look in around the variants
win_r2: numeric, the lower r2 limit to include in output, (for –r-phased and –r-unphased, this means |r|≥sqrt(0.2))
win_ninter: numeric, controls the maximum number of other variants allowed between variant-pairs in the report. Inf = off.
proxy_eaf: numeric, the minimal effect allele frequency for proxy variants. NULL = eaf filtering off.
plink2: character / path, the plink2 executable
pfile: character / path, the plink pfile set
...: other arguments (see below)
snps: a character vector (available if x is a GWAS object), a vector of rsids to ensure exist, or else try and find proxies for
then: a string (available if x is a GWAS object), either add (adds proxies to current GWAS) or subset (subsets GWAS to variants and potential proxies for variants in x)

Value

a data.table of variants and their proxies (if x is a character vector) or a GWAS object if x is a GWAS object.