get.pedmap: Generate plink-file (pedmap)

In MoBPS: Modular Breeding Program Simulator

Description

Generate a ped and map file (PLINK format) for selected groups and chromosome

Usage

get.pedmap(
  population,
  path = NULL,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  non.genotyped.as.missing = FALSE,
  use.id = FALSE
)

Arguments

population	Population list
path	Location to save pedmap-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)
non.genotyped.as.missing	Set to TRUE to replaced non-genotyped entries with "./."
use.id	Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names

Value

Ped and map-file for in gen/database/cohorts selected individuals

Examples

data(ex_pop)

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

MoBPS documentation built on Nov. 9, 2021, 5:08 p.m.