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. 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) .


Reference manual

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0.3.1 by Tom Druet, 8 months ago

Browse source code at

Authors: Tom Druet , Naveen Kumar Kadri , Amandine Bertrand and Mathieu Gautier

Documentation:   PDF Manual  

GPL-3 license

Imports foreach, doParallel, parallel, data.table, RColorBrewer, iterators

Depends on methods

Suggests knitr, rmarkdown, testthat

See at CRAN