Get proxies for variants from plink binary
get_proxies.Rd
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 aGWAS
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).