elim_conf_using_two_pts

Drops unlikely configuration phases given the two-point information
and a LOD threshold

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 

elim_conf_using_two_pts function

<dl><dt>input.seq</dt>
<dd>an object of class <code>mappoly.sequence</code>.</dd>
<dt>twopt</dt>
<dd>an object of class <code>mappoly.twopt</code></dd>
<dt>thres</dt>
<dd>threshold from which the linkage phases can be
discarded (if abs(ph_LOD) &gt; thres)</dd></dl>

Arguments

Eliminate configurations using two-point information — elim_conf_using_two_pts

<dl>

<dt>input.seq</dt>
<dd>an object of class <code>mappoly.sequence</code>.</dd>


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


<dt>thres</dt>
<dd>threshold from which the linkage phases can be
discarded (if abs(ph_LOD) &gt; thres)</dd>

</dl>

Eliminate configurations using two-point information

elim_conf_using_two_pts: Eliminate configurations using two-point information

Description

Usage

Value

Arguments