GenLib.jl

Tools for pedigree analysis.

A pure Julia port of R's GENLIB genetics and genealogical library.

• Basic functions that use the same syntax as R's GENLIB, sometimes faster than the original implementations;
• A function that computes the most recent common ancestors several magnitudes faster than gen.findMRCA in R's GENLIB;
• The fastest available implementation to compute pairwise kinship coefficients, based on the algorithm by Karigl, 1981;
• The fastest available implementation to compute a square matrix of kinship coefficients, based on the algorithms by Karigl, 1981 and Kirkpatrick et al., 2019.

The Tutorials explain how to get started using GenLib.

See the Index for the complete list of documented functions and types.

The Bibliography lists the sources used for implementing the algorithms.

julia> ]
pkg> add GenLib

julia> import GenLib as gen

julia> ped = gen.genealogy(gen.geneaJi)
A pedigree with:
29 individuals;
44 parent-child relations;
15 men;
14 women;
3 subjects;
8 generations.

julia> gen.phi(ped)
3×3 Matrix{Float64}:
 0.591797   0.371094   0.0722656
 0.371094   0.591797   0.0722656
 0.0722656  0.0722656  0.535156

julia> gen.pro(ped)
3-element Vector{Int64}:
  1
  2
 29

julia> ped[1]
ind: 1
father: 4
mother: 3
sex: 1

julia> ped[1].father
ind: 4
father: 8
mother: 6
sex: 1

julia> ped[1].father.ID
4

julia> ped[1].father.children
2-element Vector{GenLib.Individual}:
 ind: 1
father: 4
mother: 3
sex: 1
 ind: 2
father: 4
mother: 3
sex: 1