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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)

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")

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