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ReadMe.txt
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--- QTL Explorer ---
A shiny application that permits to do a simple marker QTL analysis
Yan Holtz et Alban Besnard
1 - WHAT IS QTL EXPLORER
————————————————————————
It is an application that permits to visualize QTL with modern tool : Shiny and D3.Js (called with the plot.ly package).
To see how it looks like, have a look here :
www.
You need 3 files for QTL analysis, that are the 3 input of the application :
- a genetic map
- a matrix of genotyping
- a phenotyping matrix
2 - INPUT FILES
———————————————
— 1/ Genetic Map
It gives the genetic and/or the physical position of your markers (SNP / Dart / SSR…)
3 or five columns separated with tabulations. Column fields by order :
1 - group: the chromosome or linkage group
2 - marker: markers names
3 - posi: position of the marker. Decimal = « . »
4 - group_Americain: the chromosome or linkage group given by another source (optional)
5 - posi_physique: position for this second reference (optional)
#Les deux dernières colonnes sont optionnelles (je crois)
#mais une fois dans l'appli,n'essayez pas de changer en physical si vous ne les possédez pas.
— 2/ Phenotyping
A file in the .csv format that gives the phenotyping features of your individuals.
One line per individual.
The first column gives the individual names. It names must be « geno »
Then you can add as many column that you need, each giving a phenotype : ex: size / precocity / color…
— 3/ Genotyping matrix
A file in .csv format. Each line represents an individual. Each column represents a marker, and is called with the marker name.
Then alleles must be coded A, B an - for parent1, parent2 and missing data.
vous avez d'individu.
— 4/ Example
Genetic Map :
group marker posi
1A mark1 0
1A mark2 15
1A mark3 60.3
2A mark4 0
Genotyping Matrix :
SNP;mark1;mark2;mark3;mark4;mark5;mark6;mark7;mark8;mark9;mark10
Cindy;A;A;A;A;A;A;A;B;B;B
Charles;A;B;A;B;B;B;B;B;B;B
Phenotyping :
geno;Taille;Poids;Age
Cindy;1.80;80;40
Charles;1.75;68;35
3 - HOW TO USE THE APP
——————————————————————
0- Perform a t-test on every marker for every phenotype with the script from_geno_pheno_map_to_bilan_simple_marker.R.
You can call it like that :
Script from_geno_pheno_map_to_bilan_simple_marker.R genotyping_file phenotyping_file genetic_map_file
1- Create a folder for your work. In this folder create the folder : One called SHINY_APP, where you put the server.R and the ui.R files. One where
you place your data.
Your file must be named exactly:bilan_simple_marker carte genotypage.csv phenotypage.csv
2- Open R and install the packages (available on CRAN): plotly shiny and FactoMineR
install.packages("plotly")
install.packages("shiny")
install.packages("FactoMineR")
3- Charge shiny
library(shiny)
4- Change your working directory to the folder you created
setwd("Home/my_appli")
5- Run the App !
runApp("SHINY_APP_FOR_QTL_ANALYSIS")
3 - BONUS FOR EXPRESSION
——————————————————————
#Pour voir les diférentiels d'expressions selon un marqueur donné il vous faut rajouter un fichier de compte (de préférence normalisé)
#Le seul disponible pour le moment est celui sur Dic2 Silur sur un grain immature à 300°jour.