plot.mappoly.prefpair.profiles

Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
For more detail, please see Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.

Marcelo Mollinari

mappoly

Genetic Linkage Maps in Autopolyploids

Gabriel Gesteira

Cristiane Taniguti

Jeekin Lau

Oscar Riera-Lizarazu

Guilhereme Pereira

Augusto Garcia

Zhao-Bang Zeng

Katharine Preedy

Robert Gentleman

Ross Ihaka

R Foundation 

R-core 

plot.mappoly.prefpair.profiles function

<dl><dt>x</dt>
<dd>an object of class <code>mappoly.prefpair.profiles</code></dd>
<dt>type</dt>
<dd>a character string indicating which type of graphic is plotted:
<code>"pair.configs"</code> (default) plots the preferential pairing 
profile for the pairing configurations or <code>"hom.pairs"</code> plots 
the preferential pairing profile for the homolog pairs</dd>
<dt>min.y.prof</dt>
<dd>lower bound for y axis on the probability profile graphic (default = 0)</dd>
<dt>max.y.prof</dt>
<dd>upper bound for y axis on the probability profile graphic (default = 1)</dd>
<dt>thresh</dt>
<dd>threshold for chi-square test (default = 0.01)</dd>
<dt>P1</dt>
<dd>a string containing the name of parent P1</dd>
<dt>P2</dt>
<dd>a string containing the name of parent P2</dd>
<dt>...</dt>
<dd>unused arguments</dd></dl>

Arguments

Plots mappoly.prefpair.profiles — plot.mappoly.prefpair.profiles

<dl>

<dt>x</dt>
<dd>an object of class <code>mappoly.prefpair.profiles</code></dd>


<dt>type</dt>
<dd>a character string indicating which type of graphic is plotted:
<code>"pair.configs"</code> (default) plots the preferential pairing 
profile for the pairing configurations or <code>"hom.pairs"</code> plots 
the preferential pairing profile for the homolog pairs</dd>


<dt>min.y.prof</dt>
<dd>lower bound for y axis on the probability profile graphic (default = 0)</dd>


<dt>max.y.prof</dt>
<dd>upper bound for y axis on the probability profile graphic (default = 1)</dd>


<dt>thresh</dt>
<dd>threshold for chi-square test (default = 0.01)</dd>


<dt>P1</dt>
<dd>a string containing the name of parent P1</dd>


<dt>P2</dt>
<dd>a string containing the name of parent P2</dd>


<dt>...</dt>
<dd>unused arguments</dd>

</dl>

Plots mappoly.prefpair.profiles

plot.mappoly.prefpair.profiles: Plots mappoly.prefpair.profiles

Description

Usage

Arguments