SISG 2019

Association Mapping: GWAS and Sequencing Data
Instructors: Timothy Thornton and Michael Wu

This page will feature slides, exercises, and some solutions (all to follow). Prior to the module, please install the latest and up-to-date versions of R (Version 3.6) and Plink on the laptop you will use during the summer institute. Both are free.


The following R packages from CRAN will be used and should be installed:
  • qqman
  • SKAT
The R commands below can be used to install the three CRAN R packages :

install.packages("qqman")
install.packages("SKAT")

The following R packages from Bioconductor will be used and should be installed prior to the module
  • GWASTools
  • gdsfmt
  • SNPRelate
  • GENESIS
The R commands below can be used to install the R packages from Bioconductor with the latest version of R (Version 3.6) :

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("GWASTools", "gdsfmt","SNPRelate","GENESIS"))

Slides and Exercises:

For each exercises performed in R, script files be posted following. To make them work on your computer, remember to modify file names and locations appropriately. Also note that many different 'correct' solutions are possible.



Datasets

A zipped folder with the genetic relatdness matrix (GRM) and other files for exercise 6, where a linear mixed model analysis is performed, can be downloaded here: LMM_FILES_2019.zip

All indivdiual data files below can be downloaded as a single zipped folder from dropbox.
The zipped folder can be downloaded here: SISG2019Data.zip

Before trying to read data into an R or PLINK session, we recommend looking at it first, in a text editor. Is the data comma- or tab-delimited? Does it have a 'header' row containing variable names?



Other Resources