simf1gl

Simulate genotype likelihoods of F1 individuals.

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 

simf1gl function

<dl><dt>n</dt>
<dd>Sample size.</dd>
<dt>g1</dt>
<dd>The first parent's genotype.</dd>
<dt>g2</dt>
<dd>The second parent's genotype.</dd>
<dt>rd</dt>
<dd>The read depth.</dd>
<dt>alpha</dt>
<dd>The double reduction rate.</dd>
<dt>xi1</dt>
<dd>The first parent's preferential pairing parameter.</dd>
<dt>xi2</dt>
<dd>The second parent's preferential pairing parameter.</dd></dl>

Arguments

Author

Simulate genotype likelihoods of F1 individuals. — simf1gl

<dl>

<dt>n</dt>
<dd>Sample size.</dd>


<dt>g1</dt>
<dd>The first parent's genotype.</dd>


<dt>g2</dt>
<dd>The second parent's genotype.</dd>


<dt>rd</dt>
<dd>The read depth.</dd>


<dt>alpha</dt>
<dd>The double reduction rate.</dd>


<dt>xi1</dt>
<dd>The first parent's preferential pairing parameter.</dd>


<dt>xi2</dt>
<dd>The second parent's preferential pairing parameter.</dd>

</dl>

simf1gl: Simulate genotype likelihoods of F1 individuals.

Description

Usage

Value

Arguments

Author

Examples