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Quick Start

1. Install PopGen

Invoke the package manager with ] in the REPL and use

add PopGen


2. Invoke the package

Simply run:

julia> using PopGen

3. Start playing around

To help get started, you can call ?PopGen and be greeted with some information to help you get started:

julia> ?PopGen
Population genetics analyses in Julia

A few things things you can do to get started:

Import Data
-; kwargs...)
- genepop(infile; kwargs...) or similar file-specific importer
- use available @gulfsharks or @nancycats datasets

Explore PopData
- populations(PopData) to view population information
- loci(PopData) to view locus names
- samplenames(PopData) to view sample names
- missing(PopData, by = ...) to view missing information

Manipulate PopData
- populations!(PopData, ...) to rename populations
- locationdata!(PopData, ...) to add geographical coordinates
- exclude!(PopData; kwargs...) to selectively remove data

- richness(PopData) to calculate allelic richness
- kinship(PopData, method = ...) to get pairwise relatedness of individuals
- summary(PopData) to calculate F-statistics, heterozygosity, etc.
- hwetest(PopData) to test for Hardy-Weinberg Equilibrium
- pairwisefst(PopData) to calculate FST between pairs of populations