Author: Yuting Wang, Xu Gao (Corresponding author)

Epigenome-Wide Association Study in R

easyEWAS is an R package for conducting EWAS in a unified and reproducible way. It supports Illumina methylation array platforms including 27K, 450K, EPIC v1, EPIC v2, and MSA, and provides an end-to-end workflow for modeling, batch correction, visualization, validation, enrichment, and optional DMR analysis.

The Workflow Overview of easyEWAS

Installation

Before installation, we still recommend pre-installing optional dependencies used by advanced modules.

Core dependencies by function

Function	Required packages	Notes
`batchEWAS()`	`sva`	Required for ComBat batch correction
`batchEWAS(..., parallel = TRUE)`	`sva`, `BiocParallel`	`BiocParallel` is needed only for parallel mode
`enrichEWAS()`	`clusterProfiler`, `org.Hs.eg.db`	Required for ID conversion and GO/KEGG enrichment
`enrichEWAS(plot = TRUE, plotType = "dot")`	`enrichplot`	Required for dotplot visualization
`dmrEWAS()`	`DMRcate`	Required for DMR analysis

Recommended pre-install

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install(
  c(
    "sva",
    "BiocParallel",
    "clusterProfiler",
    "org.Hs.eg.db",
    "enrichplot",
    "DMRcate"
  ),
  ask = FALSE,
  update = TRUE
)

Install from GitHub

remotes::install_github("ytwangZero/easyEWAS")

Load package

library(easyEWAS)

If you prefer installing only when needed:

batchEWAS(): BiocManager::install(c("sva", "BiocParallel"))
enrichEWAS(): BiocManager::install(c("clusterProfiler", "org.Hs.eg.db", "enrichplot"))
dmrEWAS(): BiocManager::install("DMRcate")

Citation

Please cite:

Wang Y, Jiang M, Niu S, Gao X. easyEWAS: a flexible and user-friendly R package for epigenome-wide association study. Bioinformatics Advances, 2025, 5(1): vbaf026.