vcf2treemix

converts vcfR format data to TreeMix infile

in part based on vcfR2migrate function (vcfR package)

Usage

vcf2treemix(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "treemix_infile.txt"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (TreeMix infile)

Value

nothing

Details

This function converts the vcfR object to a TreeMix formatted input file The function will remove indels, and multiallelic loci, and optionally loci with missing data

Author

Tomas Hrbek November 2022

Examples

vcf2treemix(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "TreeMix_infile.txt")
#> Error: object 'my_vcf' not found
vcf2treemix(my_vcf, ind_pop, keepers, out_file = "TreeMix_infile.txt")
#> Error: object 'my_vcf' not found
vcf2treemix(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found