Get proxies for variants from plink binary — get

Subsets GWAS to variants and potential proxies for variants in x

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

...

Additional arguments passed to methods. When x is a GWAS object, use:

snps: (character) A vector of rsids to ensure exist or find proxies for.
then: (character) Either "add" (adds proxies to the GWAS) or "subset" (restricts to selected variants and proxies).