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.
- R is available from this list of sites.
- Plink is available here: Plink 1.9 Software
The following R packages from CRAN will be used and should be installed:
- qqman
- SKAT
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
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.
- Introduction
- Session 1 : Case-Control Association Testing. Exercises [.pdf ] (R script file) ( Exercise 1 solutions ) ( Rmarkdown file for Exercise 1 solutions )
- Session 2 : Association Testing with Quantitative Traits. Exercises [.pdf ] ( R script ) ( Exercise 2 solutions ) ( Rmarkdown file for Exercise 2 solutions )
- Session 3 : Introduction to the PLINK Software for GWAS. Exercises [.pdf ] (R script file) ( PLINK Script File ) (R script file from class lab)
- Session 4 : Gene and Pathway Level Analysis of Genetic Association Studies. Exercises [.pdf ] ( PLINK and R Script file )
- Session 5 : Population Structure Inference.
Exercises [.pdf ] (R script file)
( Exercise
5 solutions ) ( Rmarkdown file for Exercise 5 solutions )
- Session 6 : GWAS in Samples with Structure. Exercises [.pdf ] ( Rmarkdown file for Calculating GRM and GETTING NULL MODEL ) ( Rmarkdown file for Running the Linear Mixed Model ) ( Updated Rmarkdown file for Running the Linear Mixed Model)
- Session 7 : Interaction Analysis. Exercises [.pdf ] ( R Script file )
- Session 8 : Introduction to Rare Variant Analysis and Collapsing Tests Supervised Burden Tests. Exercises [.pdf ] ( R Script file )
- Session 9 : Kernel (Variance Component) Tests and Omnibus Tests for Rare Variants. Exercises [.pdf ] ( R Script file )
- Session 10 : Power and Sample Size, Design Considerations, Emerging Issues. Exercises [.pdf ] ( R Script file )
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?
- bpdata.csv
- Ht.pheno
- LHON.txt
- Population_Sample_Info.txt
- SNPlistHeight.txt
- SNPlistTransferrin.txt
- Tr.pheno
- YRI_CEU_ASW_MEX_NAM.bed
- YRI_CEU_ASW_MEX_NAM.bim
- YRI_CEU_ASW_MEX_NAM.fam
- Transferrin.bim
- Transferrin.fam
- Transferrin.bed is available for download here
- Example1.bed
- Example1.bim
- Example1.fam
- Example1.Cov
- Example1.SetID
- Example1.SSD
- Example1.SSD.info
- Example1.SSD_LOG.txt
- Example1.SSD.info.TEMP.txt
- Gene1.txt
- Gene2.txt
- Gene3.txt
- Trait1.txt
- Trait2.txt
- Trait3.txt
- covC.dat
- covD.dat
- Tr_dich.pheno
- ExomeChr22.avinput
- ExomeChr22.avinput.exonic_variant_function
- ExomeChr22.avinput.variant_function
- ExomeChr22.bed
- ExomeChr22.bim
- ExomeChr22.fam
- ExomeChr22.nosex
- ExomeChr22.SetID
- ExomeChr22.tped
- ExomeChr22.tfam
- ExomeChr22.Cov
- ExomeChr22.vcf.gz
- ExomeChr22.vcf.gz.vcfidx
- Example.R
- Example.sh
- Lib.R
- 1000G-Data-Analysis.pdf
- refGene.txt
Other Resources
- A tutorial for the SNPRelate package is available here: SNPRelate Tutorial
- 2009 AJHG article by Benyamin et al for a GWAS of Transferrin
- 2016 TPB Paper on EIGENANALYSIS (PCA) for population Structure Inference and Admixture Estimation
- HapMap MXL Individual Ancestry Figure (Supervised Learning)