Save SNPDataLong object to PLINK format

Saves genotype and map data from an SNPDataLong object in PLINK format (.ped/.map and optionally binary files).

savePlink(
  object,
  path = "plink_out",
  name = "plink_data",
  run_plink = TRUE,
  chunk_size = 1000
)

Arguments

object

An object of class SNPDataLong.

path

Character. Directory where files will be saved.

name

Character. Base name for PLINK output files.

run_plink

Logical. If TRUE (default), runs PLINK1 to convert to binary files. If FALSE, only .ped and .map files are saved.

chunk_size

Integer. Number of individuals per chunk for writing .ped file (default: 1000).

Value

No return value. Files are saved to disk.

Examples

if (FALSE) { # \dontrun{
savePlink(genotypes_qc, path = "plink_out", name = "nelore_qc", run_plink = TRUE, chunk_size = 2000)
} # }