Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes
Computes the realized inbreeding coefficient
Computes the realized kinship
The result of local IBD probabilities for a pair of individuals among ...
The result of local IBD probabilities for a pair of individuals among ...
The map for local IBD probabilities for a pair of individuals among th...
Merge several zres objects generated by zoorun
Extracts the IBD probabilities from the kres object
Extracts the HBD probabilities from the zres object
Extracts the realized autozygosity from the zres object
Extracts the HBD segments from the zres object
RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozyg...
Update one main zres object with new results
Read the genotype data file
Use the ZooRoH model to estimate kinship between pairs of individuals
Define the model for the RZooRoH
Plot HBD segments identified with the ZooROH model
Plot individual curves with proportion of the genome in each HBD class...
Plot the partitioning of the genome in different HBD classes for each ...
Plot proportion of the genome associated with different HBD classes
Run the ZooRoH model
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. These 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, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324> and Druet and Gautier (2022) <doi:10.1016/j.tpb.2022.03.001>.