vcf2related

converts vcfR format data to Related infile

in part based on vcfR2genepop function (vcfR package)

Usage

vcf2related(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "related_infile.txt"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Related infile)

Value

nothing

Details

This function converts the vcfR object to a Related formatted input file The function will remove indels, and multiallelic loci, and optionally loci with missing data 'A', 'C', 'G', 'T' is 01, 02, 03, 04

Author

Tomas Hrbek April 2023

Examples

vcf2related(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "Genepop_infile.gen")
#> Error: object 'my_vcf' not found
vcf2related(my_vcf, ind_pop, keepers, out_file = "Related_infile.txt")
#> Error: object 'my_vcf' not found
vcf2related(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found