wfabc and SLIM activity
Activity by Claudia Bank, 29 January 2018
Aims of this activity
Part 1: Today’s challenge is to analyze time-serial allele-frequency data and, in collaboration with the whole group, find out which data set belongs to which of the scenarios that will be revealed in the second part of the tutorial. Analyses are done with wfabc (Foll et al. 2014; Foll et al. 2015)[which could be available here, if later needed: Dropbox or jjensenlab.org]. A Rmd-script will be run for this tutorial, which can be adapted by the participants. Finally part 1 will be concluded by a presentation & discussion of the results.
Part 2: Everyone will use SLIM (Haller and Messer 2017), which is available at this website, to recreate the scenario they believe has been going on in their data set.
In the end we will reveal the true scenarios in the data sets and discuss how to make better methods to detect/distinguish these.
Running this activity
First open your favourite browser window (Firefox, Safari, etc.) and enter the address of your Amazon instance, followed by a colon and the port number 8787 e.g.: http://ecX-XX-XXX-XXX-XXX.compute-1.amazonaws.com:8787. R-studio should then open directly in your browser. Then go to File->Open file (top left), navigate into the ~/workshop_materials/08_selection/public/ folder and select the
exercise_part_1.Rmd file.
Have a look at the text of the ~/workshop_materials/08_selection/public/exercise_part_1.Rmd file. The working environment is already set up for you on the Amazon instance: do not run any commands until line 97 . Then follow the instructions and run the chunks as described in the Rmd-file.
The challenge data, which was assigned to you can be found next to your name in the shared Google document of the AMIs.
Please open ~/workshop_materials/08_selection/public/exercise_part_2.Rmd only after finishing part 1.