8 Epigenomic studies

In this chapter, we analyze epigenomic data in the form of DNA methylation. Our aim is to identify sites where differences in methylation can help to explain phenotypic differences between individuals. Numerous methylomic datasets that are publicly available are from microarray experiments. Many methods for preprocessing data and performing association analysis are similar to those explained for transcriptomic data. However, important differences need to be taken into account, in particular, methylation of neighboring sites are correlated and, therefore, various approaches to test the association between methylomic data and phenotypic differences can be used. Some of the most common approaches are available through the Bioconductor package MEAL. Here, we demonstrate the use of the package on the GEO study of Alzheimer’s disease GSE80970. We show how to perform different analyses within a single pipeline and how to extract, evaluate and plot results.

The R code to reproduce the results and figures of this chapter can be found here.