A function to estimate the number of private alleles in each population.

Usage

Private.alleles(
  data,
  pops,
  write = FALSE,
  prefix = NULL,
  population_col = NULL,
  individual_col = NULL
)

Arguments

data: Character. String indicating the name of the vcf file or vcfR object to be used in the analysis.
pops: Character. String indicating the name of the population assignment file or dataframe containing the population assignment information for each individual in the data. This file must be in the same order as the vcf file and include columns specifying the individual and the population that individual belongs to. The first column should contain individual names and the second column should indicate the population assignment of each individual. Alternatively, you can indicate the column containing the individual and population information using the individual_col and population_col arguments.
write: Boolean. Optional argument indicating Whether or not to write the output to a file in the current working directory. This will output to files; 1) the table of private allele counts per population (named prefix_PrivateAlleles_countperpop) and 2) metadata associated with the private alleles (named prefix_PrivateAlleles_metadata). Please supply a prefix it you write files to your working directory as a best practice.
prefix: Character. Optional argument indicating a string that will be appended to file output. Please set a prefix if write is TRUE.
population_col: Numeric. Optional argument (a number) indicating the column that contains the population assignment information.
individual_col: Numeric. Optional argument (a number) indicating the column that contains the individuals (i.e., sample name) in the data.

Value

A list containing the count of private alleles in each population and the metadata for those alleles. The metadata is a list that contains the private allele and locus name for each population.

Author

Keaka Farleigh

Examples

# \donttest{
data("HornedLizard_Pop")
data("HornedLizard_VCF")
Test <- Private.alleles(data = HornedLizard_VCF, pops = HornedLizard_Pop, write = FALSE)# }
#> [1] "vcfR object detected, proceeding to formatting."
#> Formatting has finished, moving onto calculations
#> [1] "Finished private allele calculations for East"
#> [1] "Finished private allele calculations for South"
#> [1] "Finished private allele calculations for West"