get_indices_from_selected_phases

Get the indices of selected linkage phases given a 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 

get_indices_from_selected_phases function

<dl><dt>x</dt>
<dd>a data frame containing information about two markers. In
this data frame, the lines indicate the possible configuration
phases and the columns indicate the LOD for configuration phase
(ph_LOD), the recombination fraction (rf), and the LOD for
recombination fraction (rf_LOD)</dd>
<dt>thres</dt>
<dd>a threshold from which the linkage phases can be
discarded (if abs(ph_LOD) &gt; thres)</dd></dl>

Arguments

Get the indices of selected linkage phases given a threshold — get_indices_from_selected_phases

<dl>

<dt>x</dt>
<dd>a data frame containing information about two markers. In
this data frame, the lines indicate the possible configuration
phases and the columns indicate the LOD for configuration phase
(ph_LOD), the recombination fraction (rf), and the LOD for
recombination fraction (rf_LOD)</dd>


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

</dl>

Get the indices of selected linkage phases given a threshold

get_indices_from_selected_phases: Get the indices of selected linkage phases given a threshold

Description

Usage

Value

Arguments