vcf2structure

converts vcfR format data to Structure or FastStructure infile

in part based on vcfR2migrate function (vcfR package)

Usage

vcf2structure(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "structure.str",
  method = "S"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Structure infile)

method

-> Structure or FastStructure format

Value

nothing

Details

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

Author

Tomas Hrbek December 2020

Examples

vcf2structure(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "Structure_infile.str", method = "S")
#> Error: object 'my_vcf' not found
vcf2structure(my_vcf, ind_pop, keepers, out_file = "Structure_infile.str")
#> Error: object 'my_vcf' not found
vcf2structure(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found