Genomic Medicine 2018 Module 6 Lab

Module 6: Epigenetic Profiling in Disease

by Andrei Turinsky, PhD

Introduction

Description of the lab

In this module’s lab, we will use R packages to analyse epigenetic data related to disease (Down syndrome dataset extracted from Gene Expression Omnibus). We will use a custom-made R script to perform a series of exploratory data analysis tasks, such as clustering, classification, detection of differentially methylated sites and regions, and batch correction.

Local software that we will use

• A web browser
• RStudio

Tutorial

Exploratory analysis of DNA methylation dataset in R

• Create a new directory (folder) for Module 6.

• Place the provided R script into the newly created directory for Module 6.

• Place 3 data files samplesheet.csv, betas.csv and annotations.csv into the newly created directory for Module 6.

• Open the RStudio. Follow the menu File > New Project > Existing Directory, and choose your Module 6 directory to create a new R project.

• Load the R script into the RStudio.

• For the remainder of the tutorial, run the R script line by line, e.g. by pressing Ctrl-Enter or (Cmd-Enter on Mac), following the instructor. Examine the results and the script comments… until you are done!