How to perform a QTL analysis using the qtl package in R and plot the results (2 or more phenotypes)

This video shows you how to perform a QTL analysis using the program R.

There is a second part to this video, which can be found here:

This tutorial assumes you already have the following programs installed:

These programs are free of charge and can be installed on a Windows, Mac, or Linux (for instance, Ubuntu) machine.

Furthermore, this video assumes you have already installed the following R libraries: lme4, qtl, devtools, and qtlTools.

This video illustrates how to perform the analysis using a Mac, but it should work exactly the same on a Windows machine, as well as on a Linux machine (assuming you have properly installed the packages on your Linux machine).

The files utilized in this tutorial can be downloaded below. Be sure to unzip the files first, and keep them together in the same folder.

[Nica]

Hi, thank you for your video.

I am having problems.
If some of my seed lines are Heterozygous (H) for some markers. Should these seed line be excluded from analysis?

I also have some instances where we were unsure of the marker, so we wrote NC. Does this mean I need to remove the whole marker, or even the whole seed line?

How do i get around this please?

[renusharma]

hi,
Your lecture is quite informative,
can u please tell me how this file with recombination frequency is created?
It will be of great help.
Thanks!

[qonitaauliazahidah]

I try to following the syntax but it shown error when I called the data "can't find the individual ID column" could you help me?

[renusharma]

Hi
I am not getting the plot even though I am following this video on your data only but still I am unable to get any plot. Kindly help me out.

[shittuaoluniyi]

hi prof and thanks for this wonderful lecturer. I tried the scripts but I was not able to get the figures