offspring_gf_3

Calculates offspring genotype frequencies under the three-parameter model.

Provides tests for segregation distortion in F1
polyploid populations under different assumptions of meiosis.
These tests can account for double reduction, partial preferential pairing,
and genotype uncertainty through the use of genotype likelihoods.
Parallelization support is provided. Details of these methods are
described in Gerard et al. (2025a) <doi:10.1007/s00122-025-04816-z>
and Gerard et al. (2025b) <doi:10.1101/2025.06.23.661114>.
Part of this material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The
opinions, findings, and conclusions or recommendations expressed
are those of the author and do not necessarily reflect the views
of the National Science Foundation.

David Gerard

segtest

Tests for Segregation Distortion in Polyploids

Mira Thakkar

Guilherme da Silva Pereira

NSF DBI 2132247 

offspring_gf_3 function

<dl><dt>tau</dt>
<dd>Probability of quadrivalent formation</dd>
<dt>beta</dt>
<dd>Probability of double reduction given quadrivalent formation</dd>
<dt>gamma1</dt>
<dd>Probability of AA_aa pairing in parent 1</dd>
<dt>gamma2</dt>
<dd>Probability of AA_aa pairing in parent 2</dd>
<dt>p1</dt>
<dd>The first parent's genotype</dd>
<dt>p2</dt>
<dd>The second parent's genotype</dd></dl>

Arguments

Author

Calculates offspring genotype frequencies under the three-parameter model. — offspring_gf_3

<dl>

<dt>tau</dt>
<dd>Probability of quadrivalent formation</dd>


<dt>beta</dt>
<dd>Probability of double reduction given quadrivalent formation</dd>


<dt>gamma1</dt>
<dd>Probability of AA_aa pairing in parent 1</dd>


<dt>gamma2</dt>
<dd>Probability of AA_aa pairing in parent 2</dd>


<dt>p1</dt>
<dd>The first parent's genotype</dd>


<dt>p2</dt>
<dd>The second parent's genotype</dd>

</dl>

offspring_gf_3: Calculates offspring genotype frequencies under the three-parameter model.

Description

Usage

Value

Arguments

Author

Examples