Summer Institute in Statistical Genetics
Module 13: Bayesian Statistics for Genetics
Instructors: Ken Rice and Ting Ye

This page, updated throughout the course, will feature slides from our sessions, and examples for you to try.

Prior to the module, please install up-to-date versions of R and RStudio on the laptop you will use during the summer institute. Both are free.

Other software that will be useful, but only used in parts of the module:
Slides and exercises

Script files will posted following each session; these contain our R code for the exercises. To make them work on your computer, remember to modify file names and locations appropriately. Also note that many different 'correct' solutions are possible.

The module has 10 sessions, each of 90 minutes. The standard format for a session is approximately:

  • 50 minutes of lecture material (presented live, also recorded for later reference)
  • 25 minutes of code demonstrations and exercises for you to try. We strongly recommend working with other students
  • 15 minute discussion of exercises, where the instructors will present possible solutions and answer questions (also recorded)


Slides and code used in-class
Wednesday, July 19th
Time Topic Lecture Exercises/Discussion
1:30pm-3:00pm 0/1. Introductions, motivation for Bayes Slides [.pdf] Slides [.pdf], [recording] Exercises, Key [.pdf, .docx]
3:30pm-5:00pm 2. Binomial sampling, part 1 Slides [.pdf], [recording] Demo and exercises [.Rmd], Key [.pdf]
Thursday, July 20th
Time Topic Lecture Exercises/Discussion
8:30am-10:00am 3. Binomial sampling, part 2 Slides [.pdf], [recording] Demo and exercises [.Rmd], Key [.R]
10:30am-12:00pm 4. Multinomial Samples & INLA Slides [.pdf], INLA example [.R] [recording] Demo and exercises [.Rmd], Key [.pdf]
1:30pm-3:00pm 5. Linear models Slides [.pdf], [2022 recording] Exercises Script from demo [.R], Key [.pdf]
3:30pm-5:00pm 6. Model selection and averaging Slides [.pdf], Code [.R] [recording] Exercises Key [.pdf]
Friday, July 21st
Time Topic Lecture Exercises/Discussion
8:30am-10:00am 7. Mendelian Randomization Slides [.pdf], [recording] Demo and exercises [.R], Key to follow
10:30am-12:00pm 8. Meta-analysis Slides [.pdf],[recording] Exercises Script file [.R], Key [.pdf]
1:30pm-3:00pm 9. Testing and Multiple Testing Slides [.pdf], prostmat.csv, prostz.txt Demo [.Rmd] (no exercises for this session),
3:30pm-5:00pm 10. Software examples Slides [.pdf] See demo resources below

Resources for Session 10: most of the examples run the HWE example - each example is self-contained

Comments forms and attendance certificates are available here - requires SISG account.

Datasets
  • ASAgene.txt: Data for Session 2 and 3
  • diagen_bma: Data and posterior simulations for Session 6 - load into an R session with load()
  • yX_FTO: Copy of the FTO data, for Session 6 - load into an R session with load()

Other resources

Some recommended books;