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PairwiseFST.jl

PopGen.jl/src/FStatistics/PairwistFST.jl​

📦 not exported🔵 exported by PopGen.jl

🔵 Base.show​

Base.show(io::IO, data::PairwiseFST)

🔵 PairwiseFST​

PairwiseFST
    results::DataFrame
    method::String

A convenience data structure which stores the results and method of a pairwisefst analysis. The object pretty-prints a bit more information to the console, especially when doing a global pairwise FST.

🔵 pairwisefst​

pairwisefst(data::PopData; method::Function, by::String = "global", iterations::Int64)

Calculate pairwise FST between populations in a PopData object. Set iterations to a value greater than 0 to perform a single-tailed permutation test to obtain P-values of statistical significance. Use by = "locus" to perform a locus-by-locus FST for population pairs (iterations and significance testing ignored). Returns a PairwiseFST object, stores a DataFrame of the results, along with the method used to obtain the estimates.

Methods:​

  • Hudson: Hudson et al. (1992) method (only for biallelic data)
  • Nei: Nei (1987) method
  • WeirCockerham : Weir & Cockerham (1984) method (default)

Examples

data = @nancycats
wc = pairwise_fst(data, method = WeirCockerham)
wc_sig = pairwise_fst(data, iterations = 1000)