prepare_map_custom_files

Converts map information in custom format files to viewmap 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_map_custom_files function

<dl><dt>dosages</dt>
<dd>TSV or TSV.GZ file with both parents dosage information.
It should contain four columns: 1) character vector with chromosomes ID; 
2) Character vector with markers ID; 3) Character vector with parent ID; 
4) numerical vector with dosage.</dd>
<dt>phases</dt>
<dd>TSV or TSV.GZ file with phases information. It should contain:
1) Character vector with chromosome ID; 2) Character vector with marker ID;
3 to (ploidy number)*2 columns with each parents haplotypes.</dd>
<dt>genetic_map</dt>
<dd>TSV or TSV.GZ file with the genetic map information</dd>
<dt>mks_pos</dt>
<dd>TSV or TSV.GZ file with table with three columns: 1) marker ID; 
2) genome position; 3) chromosome</dd></dl>

Arguments

Converts map information in custom format files to viewmap object — prepare_map_custom_files

<dl>

<dt>dosages</dt>
<dd>TSV or TSV.GZ file with both parents dosage information.
It should contain four columns: 1) character vector with chromosomes ID; 
2) Character vector with markers ID; 3) Character vector with parent ID; 
4) numerical vector with dosage.</dd>


<dt>phases</dt>
<dd>TSV or TSV.GZ file with phases information. It should contain:
1) Character vector with chromosome ID; 2) Character vector with marker ID;
3 to (ploidy number)*2 columns with each parents haplotypes.</dd>


<dt>genetic_map</dt>
<dd>TSV or TSV.GZ file with the genetic map information</dd>


<dt>mks_pos</dt>
<dd>TSV or TSV.GZ file with table with three columns: 1) marker ID; 
2) genome position; 3) chromosome</dd>

</dl>

Converts map information in custom format files to viewmap object

prepare_map_custom_files: Converts map information in custom format files to viewmap object

Description

Usage

Value

Arguments