'Analysis of molecular traits' practical

Nov 2025

Created by Matthew Suderman matthew.suderman@bristol.ac.uk

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:

## if necessary, install these two packages
install.packages("rmarkdown")
install.packages("MatrixEQTL")

## generate html output 
library(rmarkdown)
rmarkdown::render("practical.rmd")

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

Student files

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

Dataset

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