select_haplo

internal

Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including  gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.

Cristiane Taniguti

viewpoly

A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species

Gabriel de Siqueira Gesteira

Jeekin Lau

Olivia Angelin-Bonnet

Susan Thomson

Guilherme da Silva Pereira

David Byrne

Zhao-Bang Zeng

Oscar Riera-Lizarazu

Marcelo Mollinari

select_haplo function

<dl><dt>input.haplo</dt>
<dd>character vector with selected haplotypes. It contains the information: "Trait:&lt;trait ID&gt;_LG:&lt;linkage group ID_Pos:&lt;QTL position&gt;"</dd>
<dt>probs</dt>
<dd>data.frame with first column (named `ind`) as individuals ID and next columns named with markers ID and containing the genotype probability at each marker</dd>
<dt>selected_mks</dt>
<dd>data.frame with: LG - linkage group ID; mk - marker ID; pos - position in linkage map (cM)</dd>
<dt>effects.data</dt>
<dd>output object from <code>data_effects</code> function</dd>
<dt>exclude.haplo</dt>
<dd>character vector with haplotypes to be excluded. It contains the information: "Trait:&lt;trait ID&gt;_LG:&lt;linkage group ID_Pos:&lt;QTL position&gt;"</dd></dl>

Arguments

Plot selected haplotypes — select_haplo

<dl>

<dt>input.haplo</dt>
<dd>character vector with selected haplotypes. It contains the information: "Trait:&lt;trait ID&gt;_LG:&lt;linkage group ID_Pos:&lt;QTL position&gt;"</dd>


<dt>probs</dt>
<dd>data.frame with first column (named `ind`) as individuals ID and next columns named with markers ID and containing the genotype probability at each marker</dd>


<dt>selected_mks</dt>
<dd>data.frame with: LG - linkage group ID; mk - marker ID; pos - position in linkage map (cM)</dd>


<dt>effects.data</dt>
<dd>output object from <code>data_effects</code> function</dd>


<dt>exclude.haplo</dt>
<dd>character vector with haplotypes to be excluded. It contains the information: "Trait:&lt;trait ID&gt;_LG:&lt;linkage group ID_Pos:&lt;QTL position&gt;"</dd>

</dl>

Plot selected haplotypes

select_haplo: Plot selected haplotypes

Description

Usage

Value

Arguments