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")