Module S2: Bayesian Statistics for Genetics
Instructors: Ken Rice and Steve Qin
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, June 4th |
Time |
Topic |
Lecture |
Exercises/Discussion |
1:00pm-3:00pm |
0/1. Introductions, motivation for Bayes |
Slides [.pdf] Slides [.pdf] |
Exercises, Key [.pdf] |
3:30pm-5:00pm |
2. Binomial sampling, part 1 |
Slides [.pdf] |
Demo and exercises [.Rmd], [.pdf], Key [.pdf] |
Thursday, June 5th |
Time |
Topic |
Lecture |
Exercises/Discussion |
8:30am-10:00am |
3. Binomial sampling, part 2 |
Slides [.pdf] |
Demo and exercises [.Rmd] [.pdf], Key [.R] |
10:30am-12:00pm |
4. Multinomial Samples & INLA |
Slides [.pdf], INLA example [.R] |
Demo and exercises [.Rmd] [.pdf], Key [.Rmd] [.pdf] |
1:30pm-3:00pm |
5. Linear models |
Slides [.pdf] |
Exercises Script from demo [.R], Key [.Rmd] [.pdf] |
3:30pm-5:00pm |
6. Clustering |
Slides [.pdf] |
Exercises [.Rmd] [.pdf] |
Friday, June 6th |
Time |
Topic |
Lecture |
Exercises/Discussion |
8:30am-10:00am |
7. Meta-analysis |
Slides [.pdf] |
Exercises Script file [.R] |
10:30am-12:00pm |
8. Hierarchical models |
Slides [.pdf] |
No exercises for this session |
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
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
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