Description
Exclusion-Based Parentage Assignment Using Multilocus Genotype Data.
Description
Exclusion-based parentage assignment is essential for studies in biodiversity conservation and breeding programs - Kang Huang, Rui Mi, Derek W Dunn, Tongcheng Wang, Baoguo Li, (2018), <doi:10.1534/genetics.118.301592>. The tool compares multilocus genotype data of potential parents and offspring, identifying likely parentage relationships while accounting for genotyping errors, missing data, and duplicate genotypes. 'acoRn' includes two algorithms: one generates synthetic genotype data based on user-defined parameters, while the other analyzes existing genotype data to identify parentage patterns. The package is versatile, applicable to diverse organisms, and offers clear visual outputs, making it a valuable resource for researchers.
README.md
acoRn
acoRn an open-source R package designed for exclusion-based parentage assignment. Utilizing the principles of Mendelian segregation, acoRn analyzes multilocus genotype data from potential parents and offspring to identify likely parentage relationships, while accommodating genotyping errors, missing data, and duplicate genotypes.
Installation
acoRn can be easily installed through GitHub as follows:
# install.packages("remotes")
library(remotes)
install_github("npechl/acoRn")
Usage
Synthetic genotype data generation
# load acoRn
library(acoRn)
# create mock parents dataset
parents <- create_mock_parents()
# create mock progeny dataset
offspring <- create_mock_progeny(p[[1]], fparents = 5, mparents = 5, prog = 5)
Parental assignment
# load acoRn
library(acoRn)
# example datasets
data("parents")
data("offspring")
# run acoRn
r <- acoRn(parents, offspring)
head(r)