breeding_values

Estimate breeding values - Adapted function from QTLpoly

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

breeding_values function

<dl><dt>qtl_info</dt>
<dd>data.frame with: LG - linkage group ID; Pos - position in linkage map (cM); 
Pheno - phenotype ID; Pos_lower - lower position of confidence interval; 
Pos_upper - upper position of the confidence interval; Pval - QTL p-value; h2 - herdability</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>blups</dt>
<dd>data.frame with: haplo - haplotype ID; pheno - phenotype ID; qtl - QTL ID; u.hat - QTL estimated BLUPs</dd>
<dt>beta.hat</dt>
<dd>data.frame with: pheno - phenotype ID; beta.hat - estimated beta</dd>
<dt>pos</dt>
<dd>selected QTL position (cM)</dd></dl>

Arguments

Estimate breeding values - Adapted function from QTLpoly — breeding_values

<dl>

<dt>qtl_info</dt>
<dd>data.frame with: LG - linkage group ID; Pos - position in linkage map (cM); 
Pheno - phenotype ID; Pos_lower - lower position of confidence interval; 
Pos_upper - upper position of the confidence interval; Pval - QTL p-value; h2 - herdability</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>blups</dt>
<dd>data.frame with: haplo - haplotype ID; pheno - phenotype ID; qtl - QTL ID; u.hat - QTL estimated BLUPs</dd>


<dt>beta.hat</dt>
<dd>data.frame with: pheno - phenotype ID; beta.hat - estimated beta</dd>


<dt>pos</dt>
<dd>selected QTL position (cM)</dd>

</dl>

Estimate breeding values - Adapted function from QTLpoly

breeding_values: Estimate breeding values - Adapted function from QTLpoly

Description

Usage

Value

Arguments