vcf2smartsnp

converts vcfR format data to smartsnp tabular format infile

in part based on vcfR2genlight function (vcfR package)

Usage

vcf2smartsnp(
  vcf,
  ind_pop,
  keep_pop,
  inc_missing = TRUE,
  out_file = "smartsnp_infile.txt"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (genotype table infile)

Value

nothing

Details

This function converts the vcfR object to a genotype table formatted input file For use in smartsnp, but keeps sample names as column names The function will remove indels, and multiallelic loci, and optionally loci with missing data

Author

Tomas Hrbek October 2023

Examples

vcf2smartsnp(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "SmartSNP_infile.txt")
#> Error: object 'my_vcf' not found
vcf2smartsnp(my_vcf, ind_pop, keepers, out_file = "SmartSNP_infile.txt")
#> Error: object 'my_vcf' not found
vcf2smartsnp(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found