Quick Start
1. Install PopGen
- REPL/Juno
- Jupyter/nteract
Invoke the package manager with ]
in the REPL and use
add PopGen
Invoke using Pkg
using Pkg
Pkg.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
Repository: https://www.github.com/biojulia/PopGen.jl/
Documentation: https://biojulia.net/PopGen.jl/
A few things things you can do to get started:
Import Data
- PopGen.read(filename; 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
Analyses
- 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