This repository contains materials for a one-day workshop on R/qtl and R/qtl2, to be held at the Complex Trait Community meeting in Memphis, TN, on 13 June 2017.
Participants will need to bring their own laptop computer. Mac users will need to be running a very recent version of Mac OS X: El Capitan (10.11) or Sierra (10.12). To determine your installed version, click the in the upper-left and select "About this Mac".
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Install the latest version of R, 3.4.0
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Install the latest version of RStudio, 1.0.143
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Open RStudio and install the latest version of R/qtl and R/qtlcharts by typing, at the command prompt (
>),install.packages(c("qtl", "qtlcharts")) -
Install R/qtl2 by typing
install.packages("qtl2", repos="http://rqtl.org/qtl2cran")
The workshop will take place on Tuesday, 13 June, 9am-3pm, in Room 227 of the FedEx Institute. In the morning, we'll cover R/qtl and the foundations of QTL mapping. In the afternoon, we'll cover R/qtl2.
- 8:00-9:00 Light breakfast, 2nd floor FedEx Institute
- 9:00-noon R/qtl (break 10:20 - 10:40)
- noon-1:00 Light lunch, 2nd floor FedEx Institute
- 1:00-3:00 R/qtl2 (break 1:50 - 2:10)
We'll switch back-and-forth between slides and follow-along software demonstration.
- Source for the slides for the R/qtl part in
Slides_Rqtl/(PDF:Slides_Rqtl/rqtl_workshop.pdf) - In demonstrating R/qtl, we'll follow the
Shorter tour of R/qtl.
My basic script is
Scripts/rqtl_workshop.R. Here's the version I actually typed at the workshop:Scripts/rqtl_workshop_live.R. - Source for the slides for the R/qtl2 part will be in
Slides_Rqtl2/(PDF:Slides_Rqtl2/rqtl2_workshop.pdf) - In demonstrating R/qtl2, we'll follow the
User guide.
My basic script is
Scripts/rqtl2_workshop.R. Here's the version I actually typed at the workshop:Scripts/rqtl2_workshop_live.R.
To the extent possible under law,
Karl Broman has waived all copyright and
related or neighboring rights to
“R/qtl workshop”.
This work is published from the United States.
Code is licensed under the MIT license. (More information here.)