SISG: Module 17

Module 17: Bayesian Statistics for Genetics

Instructors: Jon Wakefield and Ken Rice

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

Slides and code used in-class

Session 0, Course outline

Session 1, Introductions, motivations for Bayes, overview of Bayesian statistics

Session 2, Review of probability, binomial sampling

Session 3, Binomial sampling continued. R notes [.Rmd, .pdf]

Session 4, Linear models. R script [.R]

Session 5, Multinomial sampling. R notes [.Rmd, .pdf]

Session 6, Model selection and model averaging. R script [.R]

Session 7, Multiple testing. R notes [.Rmd, .pdf]

Session 8, Generalized linear models. R notes [.Rmd, .pdf]

Session 9, Meta-analysis. No R code for this session

Session 10, Imputation and model comparison, overview of software
Code illustrating various packages - each example is self-contained

WinBUGS example - requires installing WinBUGS. If you don't remember where to point and click, watch the (unrated) WinBUGS the Movie
R2WinBUGS and JAGS example - requires installing R and its R2WinBUGS package. For the JAGS part you will also need to install JAGS and the rjags package
Stan example - requires installing R and Windows users will also need Rtools
INLA examples - requires installing R. To get the INLA package for R, follow the non-standard procedure here

Evaluation

Please complete the evalulation. You will need the username and password used to register. Upon completing the evaluation, you will automatically get a PDF certificate of participation, for the module.

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

The R site, which includes the Comprehensive R Archive Network (CRAN) of downloads and packages
A reference card of common R commands (and a slightly longer reference card)

Some recommended books;

A First Course in Bayesian Statistical Methods (Hoff, 2009) - available free with UW login
Bayesian and Frequentist Regression Methods (Wakefield, 2013) - available from with UW login
Foulkes, Applied Statistical Genetics with R For Population-based Association Studies, 2009; this book covers a lot of the material we'll discuss, although seldom from a Bayesian point of view.

Summer Institute in Statistical Genetics

Module 17: Bayesian Statistics for Genetics Instructors: Jon Wakefield and Ken Rice This page will feature slides from our sessions, and examples for you to try. Slides and code used in-class Session 0, Course outline Session 1, Introductions, motivations for Bayes, overview of Bayesian statistics Session 2, Review of probability, binomial sampling Session 3, Binomial sampling continued. R notes [.Rmd, .pdf] Session 4, Linear models. R script [.R] Session 5, Multinomial sampling. R notes [.Rmd, .pdf] Session 6, Model selection and model averaging. R script [.R] Session 7, Multiple testing. R notes [.Rmd, .pdf] Session 8, Generalized linear models. R notes [.Rmd, .pdf] Session 9, Meta-analysis. No R code for this session Session 10, Imputation and model comparison, overview of software Code illustrating various packages - each example is self-contained WinBUGS example - requires installing WinBUGS. If you don't remember where to point and click, watch the (unrated) WinBUGS the Movie R2WinBUGS and JAGS example - requires installing R and its R2WinBUGS package. For the JAGS part you will also need to install JAGS and the rjags package Stan example - requires installing R and Windows users will also need Rtools INLA examples - requires installing R. To get the INLA package for R, follow the non-standard procedure here Evaluation Please complete the evalulation. You will need the username and password used to register. Upon completing the evaluation, you will automatically get a PDF certificate of participation, for the module. 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 The R site, which includes the Comprehensive R Archive Network (CRAN) of downloads and packages A reference card of common R commands (and a slightly longer reference card) Some recommended books; A First Course in Bayesian Statistical Methods (Hoff, 2009) - available free with UW login Bayesian and Frequentist Regression Methods (Wakefield, 2013) - available from with UW login Foulkes, Applied Statistical Genetics with R For Population-based Association Studies, 2009; this book covers a lot of the material we'll discuss, although seldom from a Bayesian point of view.
Send mail to: see Jon or Ken in class Last modified: 7/19/2016