prepare_polyqtlR

Converts polyqtlR outputs to viewqtl object

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

prepare_polyqtlR function

<dl><dt>polyqtlR_QTLscan_list</dt>
<dd>list containing results from polyqtlR <code>QTLscan_list</code> function</dd>
<dt>polyqtlR_qtl_info</dt>
<dd>data.frame containing the QTL information:LG - group ID; Pos - QTL position (cM); 
pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval;
thresh - LOD threshold applied</dd>
<dt>polyqtlR_effects</dt>
<dd>data.frame with results from <code>visualiseQTLeffects</code> polyqtlR function</dd></dl>

Arguments

Converts polyqtlR outputs to viewqtl object — prepare_polyqtlR

<dl>

<dt>polyqtlR_QTLscan_list</dt>
<dd>list containing results from polyqtlR <code>QTLscan_list</code> function</dd>


<dt>polyqtlR_qtl_info</dt>
<dd>data.frame containing the QTL information:LG - group ID; Pos - QTL position (cM); 
pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval;
thresh - LOD threshold applied</dd>


<dt>polyqtlR_effects</dt>
<dd>data.frame with results from <code>visualiseQTLeffects</code> polyqtlR function</dd>

</dl>

Converts polyqtlR outputs to viewqtl object

prepare_polyqtlR: Converts polyqtlR outputs to viewqtl object

Description

Usage

Value

Arguments