get.plink: Generate binary plink-file

In MoBPS: Modular Breeding Program Simulator

Generate binary plink-file

Description

Generate a binary plink-file for selected groups and chromosome

Usage

get.plink(
  population,
  path = NULL,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  id = NULL,
  chromosome = "all",
  non.genotyped.as.missing = FALSE,
  fam.id = FALSE,
  type = 0,
  use.id = TRUE,
  bve.pedigree.error = TRUE
)

Arguments

population	Population list
path	Location to save vcf-file
database	Groups of individuals to consider for the export
gen	Quick-insert for database (vector of all generations to export)
cohorts	Quick-insert for database (vector of names of cohorts to export)
id	Individual IDs to search/collect in the database
chromosome	Limit the genotype output to a selected chromosome (default: "all")
non.genotyped.as.missing	Set to TRUE to replaced non-genotyped entries with "./."
fam.id	Set TRUE to set the fam-ID to the individual ID
type	Set 1 to only write paternal haplotype, set 2 to only write maternal haplotype, set 0 for both (default)
use.id	Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)
bve.pedigree.error	Set to FALSE to ignore/correct for any pedigree errors

Value

binary plink-file for in gen/database/cohorts selected individuals

Examples

data(ex_pop)
data(ex_pop)

file_path <- tempdir()
get.vcf(path=file_path, ex_pop, gen=2)
file.remove(paste0(file_path, ".vcf"))

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.