eQTL and meQTL practical in R

Nov 2024

Created by Matthew Suderman [email protected]

Learning objectives

1. Prepare the data for analysis#

2. Conduct an eQTL analysis using the MatrixEQTL R package

3. Produce plots to visually inspect findings

4. (Optional) Conduct an meQTL analysis

5. (Optional) Identify trios of associated genes, CpG sites and SNPs

Generate HTML version

In R:

library(rmarkdown)
rmarkdown::render("otheromics.rmd")

To include answers, rerun render after changing show.answers to TRUE in otheromics.rmd.

Student files

• otheromics.rmd
• answers.r
• plink
• expected-outputs/.

Dataset

The dataset was prepared by running scripts/create-dataset.r.