vcf2eigenstrat

converts vcfR format data to Eigenstrat infiles

in part based on vcfR2migrate function (vcfR package)

Usage

vcf2eigenstrat(
  vcf,
  ind_pop,
  keep_pop,
  sex = "U",
  rel_pos = 0,
  inc_missing = TRUE,
  out_file = "eigenstrat_infile"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

-> population(s) of interest to include in Eigenstrat infiles (factor)

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Eigenstrat infiles)

Value

nothing

Details

This function converts the vcfR object to a Eigenstrat formatted input files When list of sexes is not provided, lists all individuals as unknown When relative position on chromosome (cM distance or similar) is not provides, list as 0 The function will remove indels, and multiallelic loci, and optionally loci with missing data

Author

Tomas Hrbek December 2022

Examples

vcf2eigenstrat(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, sex = list_of_sex, rel_pos = marker_cM_map, inc_missing = TRUE, out_file = "Eigenstrat")
#> Error: object 'my_vcf' not found
vcf2eigenstrat(my_vcf, ind_pop, keepers, out_file = "Eigenstrat")
#> Error: object 'my_vcf' not found
vcf2eigenstrat(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found