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https://github.com/gphmorin/genlib.jl
A pure Julia port of R's GENLIB genetics and genealogical library
https://github.com/gphmorin/genlib.jl
bioinformatics genealogy genetics julia julia-language pedigree
Last synced: about 1 month ago
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A pure Julia port of R's GENLIB genetics and genealogical library
- Host: GitHub
- URL: https://github.com/gphmorin/genlib.jl
- Owner: GPhMorin
- License: mit
- Created: 2023-12-18T02:33:21.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-10-09T15:47:58.000Z (about 1 month ago)
- Last Synced: 2024-10-12T22:24:44.204Z (about 1 month ago)
- Topics: bioinformatics, genealogy, genetics, julia, julia-language, pedigree
- Language: Julia
- Homepage: https://gphmorin.github.io/GenLib.jl/
- Size: 1.17 MB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# GenLib.jl
[](https://gphmorin.github.io/GenLib.jl/dev)
[](https://github.com/GPhMorin/GenLib.jl/actions/workflows/CI.yml?query=branch%3Amain)
[](https://codecov.io/gh/GPhMorin/GenLib.jl)
*Tools for pedigree analysis.*
A pure Julia port of [R's GENLIB](https://cran.r-project.org/web/packages/GENLIB/index.html) genetics and genealogical library.
## Package Features
* 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](https://gphmorin.github.io/GenLib.jl/dev/bibliography/#Karigl,-1981);
* The fastest available implementation to compute a square matrix of kinship coefficients, based on the algorithms by [Karigl, 1981](https://gphmorin.github.io/GenLib.jl/dev/bibliography/#Karigl,-1981) and [Kirkpatrick et al., 2019](https://gphmorin.github.io/GenLib.jl/dev/bibliography/#Kirkpatrick-et-al.,-2019).
## Documentation
The [Tutorials](https://gphmorin.github.io/GenLib.jl/dev/tutorials/) explain how to get started using GenLib.
See the [Index](https://gphmorin.github.io/GenLib.jl/dev/#main-index) for the complete list of documented functions and types.
The [Bibliography](https://gphmorin.github.io/GenLib.jl/dev/bibliography/) lists the sources used for implementing the algorithms.
## Installation
```julia
julia> ]
pkg> add GenLib
```
## Examples
```julia
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
```