RZooRoH - Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. This rate is called the "rate of coancestry change". The HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions called also rates of coancestry change; mixing proportions related to the inbreeding rate per layer or generation), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. Functions also allow to compute identity-by-descent (IBD) between pairs of haplotypes, to estimate kinship between pairs of individuals and to predict inbreeding in the future progeny of a genotyped couple. The current model is fully described in Druet and Gautier (2022) <doi:10.1016/j.tpb.2022.03.001>. The model and its properties were originally presented in Druet and Gautier (2017) <doi:10.1111/mec.14324>. Extension to IBD and kinship analyses is described in Forneris et al. (2025) <doi:10.1111/1755-0998.14068>.