10.2 Analyzing DNA methylation data

For the remainder of this chapter, we will explain how to do DNA methylation analysis using R. The analysis process is somewhat similar to the analysis patterns observed in other sequencing data analyses. The process can be chunked to four main parts with further sub-chunks:

  1. Processing raw data
  • Quality check
  • Alignment and post-alignment processing
  • Methylation calling
  • Filtering bases
  1. Exploratory analysis
  • Clustering
  • PCA
  1. Finding interesting regions
  • Differential methylation
  • Methylation segmentation
  1. Annotating interesting regions
  • Nearest genes
  • Annotation with other genomic features
  • Integration with other quantitative genomics data