How to perform r/qtl to analyze phenotye and genotype data

Hello everyone!

I am a beginner here, I have around 100 phenotype data and around 1000 marker of genotype data.
Here, I have to analyze where the responsible loci from both of my data by performing QTL analysis. To be honest, I have not know yet about this. I am trying to find put certain literature in Google or Youtube but they were difficult to understand.
Could someone help me? I think I can use q/QTL packages but I am sorry, I am beginner here as I said above.
If there is or are someone who want to help me to write the scripts, I really appreciated it.
Thanks!

Your task comes in three parts.

Of these, the most important is understanding the question of what a QTL is:

a quantitative trait locus – a genetic locus that influences a quantitative trait

The second task is getting a working R system up and running on your workstation.

The third task is using the software. You probably want qtl2, which has an free, online full-day tutorial, for which you will need to

  • Understand fundamental genetic principles
  • Know how to access files not in the working directory by specifying the path
  • Know how to install a R package
  • Know how to assign a value to a variable
  • Know how to apply a built-in function

This site will be able to help you with your installation questions (please start a new topic). Although there may be members of this community who understand qtl2, you will find a more focused site here on the topic.