vcf2migrate

converts vcfR format data to MigrateN infile

adapted vcfR2migrate function (vcfR package) to allow for inclusion of missing data in Migrate output

converts vcfR format data to MigrateN infile

adapted vcfR2migrate function (vcfR package) to allow for inclusion of missing data in Migrate output

Usage

vcf2migrate(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "migrateN_infile.txt",
  method = "N"
)

vcf2migrate(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "migrateN_infile.txt",
  method = "N"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (MigrateN infile)

method

-> classic or het format

Value

nothing

nothing

Details

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

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

Author

Tomas Hrbek August 2020

Examples

vcf2migrate(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "MigrateN_infile.txt", method = "N")
#> Error: object 'my_vcf' not found
vcf2migrate(my_vcf, ind_pop, keepers, out_file = "MigrateN_infile.txt")
#> Error: object 'my_vcf' not found
vcf2migrate(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found

vcf2migrate(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "MigrateN_infile.txt")
#> Error: object 'my_vcf' not found
vcf2migrate(my_vcf, ind_pop, keepers, out_file = "MigrateN_infile.txt")
#> Error: object 'my_vcf' not found
vcf2migrate(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found