inst/testcodes/GEM_demo.R

In panhongNTU/GEM: GEM: fast association study for the interplay of Gene, Environment and Methylation

##################### DATA

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 = 1e-4

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)