vcf2genepop

converts vcfR format data to Genepop infile

includes population names that can be ready by read_genepop

in part based on vcfR2migrate function (vcfR package)

Usage

vcf2genepop(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "genepop_infile.txt"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

-> population(s) of interest to include in Genepop infile (factor)

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Genepop infile)

Value

nothing

Details

This function converts the vcfR object to a Genepop formatted input file This function labels populations. To read labeled populations use "read_genepop" function The function will remove indels, and multiallelic loci, and optionally loci with missing data 01, 02, 03, 04 is 'A', 'C', 'G', 'T'

Author

Tomas Hrbek January 2021

Examples

vcf2genepop(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "Genepop_infile.gen")
#> Error: object 'my_vcf' not found
vcf2genepop(my_vcf, ind_pop, keepers, out_file = "Genepop_infile.gen")
#> Error: object 'my_vcf' not found
vcf2genepop(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found