Description

This package allows the visualization of the methylation scores at CPG level in a defined genome region to perform a differential methylation analysis. Those values are represented as a heatmap and a line plot grouped by a factor, together with the gene annotation, the detected DMRs, and (optionally) the overlapping enhancers.

Dependencies

# Gviz
BiocManager::install("Gviz")

# hg38
BiocManager::install("org.Hs.eg.db")
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")

Installation

library(devtools)
devtools::install_github("raulsanzr/cpgplot")

Usage

cpgplot(genome="hg38", chr="chr11", start=27015473, end=27015991, sites=CpGs, regions=DMR.list, group=metadata$Condition)

Author

Raúl Sanz (2022)