simgl

Provide a vector of genotype counts and this will return a matrix of
genotype log-likelihoods.

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 

simgl function

<dl><dt>nvec</dt>
<dd>A vector of counts. <code>nvec[k]</code> is the number of folks with a genotype of k-1.</dd>
<dt>rd</dt>
<dd>Read depth. Lower is more uncertain.</dd>
<dt>seq</dt>
<dd>Sequencing error rate. Higher means more uncertain.</dd>
<dt>bias</dt>
<dd>Bias. 1 means no bias.</dd>
<dt>od</dt>
<dd>Overdispersion. Typical value is like 0.01. Higher means more uncertain.</dd></dl>

Arguments

Author

Simulate genotype (log) likelihoods from genotype counts — simgl

<dl>

<dt>nvec</dt>
<dd>A vector of counts. <code>nvec[k]</code> is the number of folks with a genotype of k-1.</dd>


<dt>rd</dt>
<dd>Read depth. Lower is more uncertain.</dd>


<dt>seq</dt>
<dd>Sequencing error rate. Higher means more uncertain.</dd>


<dt>bias</dt>
<dd>Bias. 1 means no bias.</dd>


<dt>od</dt>
<dd>Overdispersion. Typical value is like 0.01. Higher means more uncertain.</dd>

</dl>

simgl: Simulate genotype (log) likelihoods from genotype counts

Description

Usage

Value

Arguments

Author

Examples