Introduction

EpiMethEx 2.0 is a R package that perform DNA methylation analysis for the identification of DNA methylation (methDNA) clusters using Infinium HumanMethylation450 data. CG probeset clustering analyses are also performed considering the correlation data between CG methDNA status and expression level of relative gene, as well as the Beta difference values computed between comparison groups (e.g. tumor vs normal, tumor vs tumor). Integrated analysis may be executed combining methDNA, correlation, and Beta difference CG clusters. EpiMethEx 2.0 analyses were performed on TCGA datasets (Methylation450k and IlluminaHiSeq) of 33 different tumor types and a pool of normal samples retrieved from each cohort. The methDNA and gene expression test datasets, as well as the annotation data of CG probesets and CG clusters, are available in EpiMethEx 2.0 R package, while the full datasets are reported on Zenodo (https://zenodo.org/uploads/14066730). EpiMethEx 2.0 may be used for customized analyses of other datasets including pathological a physiological conditions.

Installation

Download the EpiMethEx 2.0 compressed installation file: Compressed installation file of EpiMethEx 2.0 package is available on https://www.epimethex.unict.it/ and as a supplementary file on publication.

Run the following command:

install.packages("path/to/ EpiMethEx2.0_0.1.0.tar.gz", repos = NULL, type = "source")

or run the code the installation from GitHub:

# Install devtools if not already installed
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
# Load devtools
library(devtools)
# Install the package from GitHub
install_github("Saverio-Candido/EpiMethEx-2.0")
# Load the installed package
library(EpiMethEx2.0)

EpiMethEx 2.0 functions

EpiMethEx 2.0 package include the following functions to perform clustering analyses:

CGclustAnn: Clustering of CG probesets based on Genomic Position, RefGene Name, or RefGene Annotation

methDNAcluster: Clustering of CG probesets according to methDNA median levels

corrCluster: Clustering of CG probesets according to correlation median levels

betaDiffcluster: Clustering of CG probesets according to Beta difference median levels

integrCluster: Integration of methDNA, Corr, and betaDiff CG clusters

A detailed description of each function is provided in the Help Pages section

Test datasets

The EpiMethEx2.0 functions may be tested in Help Pages section using the required test datasets:

cgAnnotation

CGclusterAnn_Pos

CGclusterAnn_Name

CGclusterAnn_Accession

methDNAmatrix

corrMatrix

diffExprMatrix

betaDiffmatrix

methDNAclusters

corrClusters

betaDiffclusters

Each test dataset includes only the data relative to chr1 as an example.

# Use this code to visualize the test datasets (replace "TestDataset" with the selected test dataset)
head(TestDataset)