Extract an LD matrix from a reference panel using plink 1.9

Extract an LD matrix from a reference panel using plink 1.9

Usage

plink_extract_ld(
  df,
  snp_col,
  effect_allele_col,
  metric = "r",
  bfile,
  threads = 1,
  memory = 16000,
  plink_bin
)

Arguments

df

Dataframe containing variants to be included in the LD matrix; must contain SNP identifier and effect allele

snp_col

Name of column containing SNP identifiers

effect_allele_col

Name of column containing effect alleles (used when considering signed measures of LD like r)

metric

LD metric - either r (which will return a signed correlation matrix) or r2 (which will return squared correlations)

bfile

Path to plink bfile that will be used to extract LD

threads

Number of threads (default = 1)

memory

Memory limit (default = 16000 MB)

plink_bin

Path to plink executable

Value

A square matrix containing the pairwise correlations between genetic variants

Examples

if (FALSE) {
plink_extract_ld(df, snp_col, effect_allele_col, metric = "r", bfile = "/path/to/reference/panel/", plink_bin = "/path/to/plink1.9")
}