GEM

Gene, Environment and Methylation (GEM): A tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment

Installation

Install from Bioconductor

Currently, the GEM package has been submitted to Bioconductor and under review. Once the package is on Bioconductor, you can install the package with following commands:

## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("GEM")

Install from github

## install dependent packages
if(!require("methods")){
    install.packages("methods")
}
if(!require("ggplot2")){
    install.packages("ggplot2")
}
if(!require("Rcpp")){
    install.packages("Rcpp")
}
if(!require("digest")){
    install.packages("digest")
}
if(!require("devtools")){
    install.packages("devtools")
}

## install gem package
devtools::install_github("fastGEM/GEM")

Launch the GUI

library(GEM)
GEM_GUI()

Example codes

library(GEM)
DATADIR = system.file('extdata',package='GEM')
RESULTDIR = getwd()

env_file_name = paste(DATADIR, "env.txt", sep = .Platform$file.sep)
covariates_file_name = paste(DATADIR, "cov.txt", sep = .Platform$file.sep)
covariates_file_name_gxe = paste(DATADIR, "gxe.txt", sep = .Platform$file.sep)
methylation_file_name = paste(DATADIR, "methylation.txt", sep = .Platform$file.sep)
snp_file_name = paste(DATADIR, "snp.txt", sep = .Platform$file.sep)

Emodel_pv = 1
Gmodel_pv = 1e-04
GxEmodel_pv = 1

Emodel_result_file_name = paste(RESULTDIR, "Result_Emodel.txt", sep = .Platform$file.sep)
Gmodel_result_file_name = paste(RESULTDIR, "Result_Gmodel.txt", sep = .Platform$file.sep)
GxEmodel_result_file_name = paste(RESULTDIR, "Result_GxEmodel.txt", sep = .Platform$file.sep)

Emodel_qqplot_file_name = paste(RESULTDIR, "QQplot_Emodel.jpg", sep = .Platform$file.sep)

GEM_Emodel(env_file_name, covariates_file_name, methylation_file_name, Emodel_pv, Emodel_result_file_name,Emodel_qqplot_file_name)

GEM_Gmodel(snp_file_name, covariates_file_name, methylation_file_name, Gmodel_pv, Gmodel_result_file_name)

GEM_GxEmodel(snp_file_name, covariates_file_name_gxe, methylation_file_name, GxEmodel_pv, GxEmodel_result_file_name)