Baypass

The Baypass software is an increasingly common method to use to identify putative outlier loci in population datasets. The input file format is a matrix of loci (rows) x allele counts per population (columns). This format is not suitable for most other applications, so it cannot be read into PopGen.jl, but we offer a convenience function to write PopData into this format so you can use Baypass externally.

baypass

baypass(data::PopData; filename::Union{String, Nothing} = nothing)

Convert a PopData object into a Baypass-format matrix. The input format for the Baypass software requires biallelic data. By default, it returns just the Baypass-format matrix; use the keyword argument filename to specify a file to write the matrix to. This function does not perform a Baypass analysis, but instead creates the input matrix necessary for it.

The matrix specification is:

• rows = loci
  • each row is a different locus
• columns = allele counts per population
  • each pair of columns correspond to the alleles' counts (2 alleles, 2 columns) for a population
  • as a result, there should be 2 × n_populations columns
  • e.g. row 1, columns 1:2 are the allele counts for locus 1 in population 1

Keyword arguments

• filename: a String of the name of the output file. If nothing, then this function just returns the Baypass input matrix without writing to a file. (default: nothing)

Example

julia> sharks = @gulfsharks;

julia> dropmultiallelic!(sharks)

julia> baypass(sharks, filename = "gulfsharks.baypass") ;