get_rf_from_list

Get the recombination fraction for a sequence of markers given an
object of class <code>mappoly.twopt</code> and a list
containing the linkage phase configuration. This list can be found
in any object of class <code>two.pts.linkage.phases</code>, in
x$config.to.test$'Conf-i', where x is the object of class
<code>two.pts.linkage.phases</code> and i is one of the possible
configurations.

internal

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 

get_rf_from_list function

<dl><dt>twopt</dt>
<dd>an object of class <code>mappoly.twopt</code></dd>
<dt>ph.list</dt>
<dd>a list containing the linkage phase configuration. This
list can be found in any object of class
<code>two.pts.linkage.phases</code>, in x$config.to.test$'Conf-i',
where x is the object of class <code>two.pts.linkage.phases</code>
and i is one of the possible configurations.</dd></dl>

Arguments

Get the recombination fraction for a sequence of markers given an
object of class mappoly.twopt and a list
containing the linkage phase configuration. This list can be found
in any object of class two.pts.linkage.phases, in
x$config.to.test$'Conf-i', where x is the object of class
two.pts.linkage.phases and i is one of the possible
configurations. — get_rf_from_list

<dl>

<dt>twopt</dt>
<dd>an object of class <code>mappoly.twopt</code></dd>


<dt>ph.list</dt>
<dd>a list containing the linkage phase configuration. This
list can be found in any object of class
<code>two.pts.linkage.phases</code>, in x$config.to.test$'Conf-i',
where x is the object of class <code>two.pts.linkage.phases</code>
and i is one of the possible configurations.</dd>

</dl>

Get the recombination fraction for a sequence of markers given an
object of class <code>mappoly.twopt</code> and a list
containing the linkage phase configuration. This list can be found
in any object of class <code>two.pts.linkage.phases</code>, in
x$config.to.test$'Conf-i', where x is the object of class
<code>two.pts.linkage.phases</code> and i is one of the possible
configurations.

Description

Usage

Value

Arguments