Calculation of IBD Probabilities

For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (< https://www.jstor.org/stable/29713>) and Huang (). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

statgenIBD

statgenIBD is an R package for calculating Identity By Descent (IBD) probabilities for biparental, three and four-way crosses. Calculations are based on Hidden Markov Models (HMM) and inheritance vectors. The HMM calculations are implemented in Rcpp/C++.

For more complicated pedigrees RABBIT can be used to calculate the IBDs.

Installation

• Install from CRAN:

install.packages("statgenIBD")

• Install latest development version from GitHub (requires remotes package):

remotes::install_github("Biometris/statgenIBD", ref = "develop", dependencies = TRUE)