Module 6: Epigenetic Profiling in Disease
by Andrei Turinsky, PhD
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
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.
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!