inheritance_space

The <code>inheritance_space</code> function determines the space of IBD vectors for a pedigree.
This is mostly for internal use but may be interesting by itself.

Identity by Descent (IBD) distributions in pedigrees. A Hidden Markov
Model is used to compute identity coefficients, simulate IBD segments and
to derive the distribution of total IBD sharing and segment count across
chromosomes. The methods are applied in Kruijver (2025)
<doi:10.3390/genes16050492>. The probability that the total IBD sharing
is zero can be computed using the method of Donnelly (1983)
<doi:10.1016/0040-5809(83)90004-7>.

Maarten Kruijver

ibdsegments

Identity by Descent Probability in Pedigrees

inheritance_space function

<dl><dt>pedigree</dt>
<dd>Pedigree in <code>pedtools::ped</code> form.</dd>
<dt>ids</dt>
<dd>Ids for which IBD is observed. Default is <code>pedtools::leaves(pedigree)</code>.</dd>
<dt>states</dt>
<dd>One of <code>"ibd"</code> (default), <code>"kappa"</code>, <code>"identity"</code> or <code>"detailed"</code>.</dd>
<dt>exploit_symmetries</dt>
<dd>Should symmetries be used to reduce to state space?
This can be set to <code>FALSE</code> for debugging purposes.</dd></dl>

Arguments

Inheritance space for pedigree — inheritance_space

<dl>

<dt>pedigree</dt>
<dd>Pedigree in <code>pedtools::ped</code> form.</dd>


<dt>ids</dt>
<dd>Ids for which IBD is observed. Default is <code>pedtools::leaves(pedigree)</code>.</dd>


<dt>states</dt>
<dd>One of <code>"ibd"</code> (default), <code>"kappa"</code>, <code>"identity"</code> or <code>"detailed"</code>.</dd>


<dt>exploit_symmetries</dt>
<dd>Should symmetries be used to reduce to state space?
This can be set to <code>FALSE</code> for debugging purposes.</dd>

</dl>

inheritance_space: Inheritance space for pedigree

Description

Usage

Value

Arguments

Examples