vcf2df

converts vcfR format data to DataFrame infile

adds last column of an individual's group origin

motivated to provide a dataframe for plotting PCA results

for use by modified PCA function from adegenet

Usage

vcf2df(
  vcf,
  ind_pop,
  keep_pop,
  alleles = TRUE,
  inc_missing = TRUE,
  out_file = "dataframe_infile.txt"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

alleles

-> record data as alleles (GATC) or SNPs (012) (logical)

inc_missing

-> include missing data (logical)

Value

nothing

Details

This function converts the vcfR object to a DataFrame formatted input file This function adds group (population) membership as last column The function will remove indels, and multiallelic loci, and optionally loci with missing data

Author

Tomas Hrbek December 2022

Examples

vcf2df(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, alleles = TRUE, inc_missing = TRUE, out_file = "dataframe_infile.txt")
#> Error: object 'my_vcf' not found
vcf2df(my_vcf, ind_pop, keepers, out_file = "dataframe_infile.txt")
#> Error: object 'my_vcf' not found
vcf2df(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found