README.md

In YenWenWang/HapDipKinship: HapDipKinship: Kinship estimation in haploid-diploid populations

HapDipKinship

This is a package containing algorithms, exKING-robust and KIMGENS, to estimate kinship in haploid-diploid mixed populations. These algorithms are strongly inspired by KING-robust.

Installation

To install this package, run

devtools::install_github("YenWenWang/HapDipKinship")

Kinship estimation

This package includes algorithms, exKING-robust and KIMGENS, to estimate diploid-diploid, diploid-haploid and haploid-haploid kinships. Example will be given below in simulations.

Simulations

This package also allows to simulate haplodiploidy ancestry (e.g. Hymenoptera). Alternation of generations (e.g. algae) is still under development.

We first simulate a population with three ancestral subpopulations.

ancestrygenomatrix<-PopulationSim(1000,c(0.05,0.15,0.25))

Say we want to draw individuals following either two of the Dirichlet distribution: - Dir(6,2,0.3) - Dir(2,6,0.3)

We run

ancestry<-matrix(c(6,2,0.3,2,6,0.3),nrow=3)

Then, we can simulate the pedigree. We provide an example pedigree:

(drawn with R package kinship2)

Using the given pedigree, we can simulate with:

pedigreegeno<-HapdipPedigreeSim(ancestrygenomatrix, pedigree, ancestry)

One can subset pedigreegeno, but we will use it directly.

ploidy<-data.frame(id=pedigree$id,ploidy=ifelse(pedigree$sex=="F",2,1))
kins<-kinship(pedigreegeno,ploidy)

Reference

Wang, Y-W and Ané, C. 2022. KIMGENS: A novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure. Bioinformatics 38(11):3044-3050.

YenWenWang/HapDipKinship documentation built on Jan. 20, 2025, 10:09 a.m.