Get LD matrix using local plink binary and reference dataset

Usage

ld_matrix_local(
  variants,
  bfile,
  plink_bin,
  with_alleles = TRUE,
  tmpdir = tempdir(),
  threads = NULL,
  memory = NULL
)

variants: List of variants (rsids)
bfile: Path to bed/bim/fam ld reference panel
plink_bin: Specify path to plink binary. Default = NULL. See https://github.com/MRCIEU/genetics.binaRies for convenient access to plink binaries
with_alleles: Whether to append the allele names to the SNP names. Default: TRUE
tmpdir: Directory in which to write the temporary files used by plink. Default = tempdir()
threads: Number of threads plink may use, passed as --threads. Default = NULL, plink's own default (all available cores)
memory: Memory in MiB plink may reserve, passed as --memory. Default = NULL, plink's own default (half the system's RAM)

data frame