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HardyWeinberg.jl

PopGen.jl/src/HardyWeinberg.jl​

πŸ“¦ not exportedπŸ”΅ exported by PopGen.jl

πŸ“¦ _chisqlocus​

_chisqlocus(locus::T) where T <: GenotypeArray

Calculate the chi square statistic and p-value for a locus Returns a tuple with chi-square statistic, degrees of freedom, and p-value.

πŸ”΅ hwetest​

hwetest(data::PopData; by_pop::Bool = false; correction = "none")

Calculate chi-squared test of HWE for each locus and returns observed and expected heterozygosity with chi-squared, degrees of freedom and p-values for each locus. Use by_pop = true to perform this separately for each population (default: by_pop = false) and return a NamedTuple of DataFrames with the names corresponding to the population names. Use correction = to specify a P-value adjustment method for multiple testing.

correction methods (case insensitive)

  • "bonferroni" : Bonferroni adjustment
  • "holm" : Holm adjustment
  • "hochberg" : Hochberg adjustment
  • "bh" : Benjamini-Hochberg adjustment
  • "by" : Benjamini-Yekutieli adjustment
  • "bl" : Benjamini-Liu adjustment
  • "hommel" : Hommel adjustment
  • "sidak" : Ε idΓ‘k adjustment
  • "forwardstop" or "fs" : Forward-Stop adjustment
  • "bc" : Barber-CandeΜ€s adjustment

Example

hwetest(@gulfsharks, correction = "bh")
hwetest(@gulfsharks, by_pop = true, correction = "bh")