chisq_gl

chisq_gl4

Calculates the MLE genotype and runs a chi-squared test assuming
no double reduction and no preferential pairing.

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 

chisq_gl function

<dl><dt>gl</dt>
<dd>A matrix of offspring genotype log-likelihoods. The rows index the
individuals and the columns index the possible genotypes. So
<code>gl[i, k]</code> is the offspring genotype log-likelihood for individual i and
genotype k-1.</dd>
<dt>g1</dt>
<dd>The first parent's genotype.</dd>
<dt>g2</dt>
<dd>The second parent's genotype.</dd></dl>

Arguments

<ul>
<li><code>chisq_gl4()</code>: Alias for chisq_gl, for backwards compatibility.</li>
</ul>

Functions

Author

Chi-Sq for GL — chisq_gl

<dl>

<dt>gl</dt>
<dd>A matrix of offspring genotype log-likelihoods. The rows index the
individuals and the columns index the possible genotypes. So
<code>gl[i, k]</code> is the offspring genotype log-likelihood for individual i and
genotype k-1.</dd>


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


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

</dl>

chisq_gl: Chi-Sq for GL

Description

Usage

Value

Arguments

Functions

Author

Examples