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

easyEWAS can now be installed from CRAN or GitHub. For most users, we recommend the CRAN release. We also recommend pre-installing optional dependencies used by advanced modules.

Install from CRAN (recommended)

install.packages("easyEWAS")

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 (development version)

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

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.

Welcome to easyEWAS!