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 up-to-date versions of R 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
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 [.doc , .pdf ] (R script file)
- Session 2 : Association Testing with Quantitative Triats. Exercises [.doc , .pdf ] (R script file)
- Session 3 : Introduction to the PLINK Software for GWAS. Exercises [.doc , .pdf ] (R script file) ( PLINK Script File )
- Session 4 : Gene and Pathway Level Analysis of Genetic Association Studies. Exercises [.pdf ] ( PLINK and R Script file )
- Session 5 : Population Structure Inference. Exercises [.doc , .pdf ] (R script file)
- Session 6 : GWAS in Samples with Structure. Exercises [.doc , .pdf ] (R script file)
- Session 7 : Introduction to Rare Variant Analysis and Collapsing Tests. Exercises [.pdf ] ( R Script file )
- Session 8 : Supervised Burden Tests and Variance Component Test for Rare Variants. Exercises [.pdf ] ( R Script file )
- Session 9 : Omnibus Tests, Weighting, Design Considerations. Exercises [.pdf ] ( R Script file )
- Session 10 : Gene Environment Interactions, Meta Analysis, Emerging Issues. Exercises [.pdf ] ( R Script file )
Datasets - in alphabetical order
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
- SNPlistTransferrin.txt
- Tr.pheno
- YRI_CEU_ASW_MEX_NAM.bed
- YRI_CEU_ASW_MEX_NAM.bim
- YRI_CEU_ASW_MEX_NAM.fam
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
- HapMap MXL Individual Ancestry Figure (Supervised Learning)
Send mail to: see Mike or Tim in class
Last modified: 7/14/2015
Last modified: 7/14/2015