get.haplo: Derive haplotypes of selected individuals

In MoBPS: Modular Breeding Program Simulator

Derive haplotypes of selected individuals

Description

Function to derive haplotypes of selected individuals

Usage

get.haplo(
  population,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  id = NULL,
  chromosome = "all",
  export.alleles = FALSE,
  non.genotyped.as.missing = FALSE,
  use.id = TRUE,
  array = NULL,
  remove.missing = TRUE
)

Arguments

population	Population list
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")
export.alleles	If TRUE export underlying alleles instead of just 012
non.genotyped.as.missing	Set to TRUE to replace non-genotyped markers with NA
use.id	Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)
array	Use only markers available on the array
remove.missing	Remove markers not genotyped in any individual from the export

Value

Haplotype data for in gen/database/cohorts selected individuals

Examples

data(ex_pop)
haplo <- get.haplo(ex_pop, gen=2)

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