cumkin

Computes the realized kinship with respect to a base population by summing the
relatedness from all classes with a rate lower or equal to the threshold T.
This amounts to set the base population approximately 0.5*T generations ago.
Classes with a higher rate are then no longer considered as IBD.

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>.

Tom Druet

RZooRoH

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

Naveen Kumar Kadri

Amandine Bertrand

Mathieu Gautier

cumkin function

<dl><dt>kres</dt>
<dd>The name of the kres object created by the zoorun function.</dd>
<dt>T</dt>
<dd>The value chosen to define the base population. When T is not
provided, all classes are considered to estimate the kinship.</dd></dl>

Arguments

Computes the realized kinship — cumkin

<dl>

<dt>kres</dt>
<dd>The name of the kres object created by the zoorun function.</dd>


<dt>T</dt>
<dd>The value chosen to define the base population. When T is not
provided, all classes are considered to estimate the kinship.</dd>

</dl>

cumkin: Computes the realized kinship

Description

Usage

Value

Arguments