MoBPS (version 1.13.1)

get.haplo: 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
)

Value

Haplotype data for in gen/database/cohorts selected individuals

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

Examples

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