MATH-493: GWAS-extras + data files

This folder contains functions from the genABEL package (no longer available) and data that will help with your GWAS analysis. For instructions and code, please follow the tutorial available at (the paper):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019244

https://github.com/AAlhendi1707/GWAS

OR the updated version at

https://pbreheny.github.io/adv-gwas-tutorial/index.html

In the genome-wide association analysis section of the tutorial, you will get either a warning or an error about the genABEL package. Instead of loading genABEL, ignore the error/warning and source the functions ztransform, rntransform, estlambda and GWAA.R (assuming those .R files are in your R working directory):

# Phenotype data preparation

# library(GenABEL)
source("ztransform.R")
source("rntransform.R")
source("estlambda.R")
source("GWAA.R")

NEW: If you are using R 4.0.x on a mac, you may get an error when you execute the GWAA function. If that happens, you should downgrade R to 3.6.0 (for example) and see if that works. If you still have problems, please contact me and we will try to work it out.

NOTE: You do NOT have to do the very last part (Regional Association)

- GWAS-extras
- GWASTutorial_Files.zip