README.md

In isglobal-brge/methyTools: EwAS: quality control, meta-analysIs and EnRichment

EASIER

EwAS: quality control, meta-analysIs and EnRichment

The EASIER package performs epigenetic wide-association study (EWAS) downstream analysis:

• Quality control of EWAS results
• Folders: input and ouput
• Configuration: array type, sample, ethnic, exclusion CpGs criteria
• CpG filtering selection -> list of CpGs filtered and reason
• QC with summaries -> summary SE, Beta, lambda, significatives…
• QC with plots -> QQplot, Distribution plot, precision plot, …
• CpG annotation and adjustment -> QCed EWAS results file
• Meta-analysis of EWAS results (using GWAMA)
• Folders: input and output
• Link to GWAMA
• Format QCed EWAS results file
• Run GWAMA -> EWAS meta-analysis results file
• Meta-analysis with summaries
• Meta-analysis with plots -> Heterogeneity plot, distribution plots, QQ-plots, Volcano plots, Manhattan plots andForest plots,
• Functional enrichment (pathway and molecular enrichments)
• GO and KEGG and MolSig
• Pathways with Molecular Signatures Database (MSigDB)
• ConsensusPath Data Base
• Gene relative position
• CpG island relative position
• Specific for Blood :
  • 15 ROADMAP chromatine states
  • eQTM enrichment with data from Helix : Identification of blood autosomal cis-expression quantitative trait methylation (cis-eQTMs) in children
• Specific for Placenta :
  • ROADMAP chromatine states Fetal Placenta 15 and 18
  • Partially methylated domains (PMDs)
  • Impreinted regions

Install :

Install in R as :

# Install devtools
install.packages("devtools")
library(devtools)

# Install required packages 
devtools::source_url("https://raw.githubusercontent.com/isglobal-brge/EASIER/HEAD/installer.R")

# Install EASIER R package
devtools::install_github("isglobal-brge/EASIER@HEAD")

isglobal-brge/methyTools documentation built on June 9, 2025, 1:38 p.m.