## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(dpi = 300) knitr::opts_chunk$set(cache=FALSE) ## ----eval=FALSE--------------------------------------------------------------- # ## try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("GEM") ## ----results='hide'----------------------------------------------------------- require(GEM) ## ----eval=FALSE--------------------------------------------------------------- # GEM_GUI() ## ----------------------------------------------------------------------------- DATADIR = system.file('extdata',package='GEM') dir(path = DATADIR) ## ----echo=FALSE--------------------------------------------------------------- read.table(paste(DATADIR, "cov.txt", sep = .Platform$file.sep), header = TRUE, row.names = 1)[1, 1:10] ## ----echo=FALSE--------------------------------------------------------------- read.table(paste(DATADIR, "env.txt", sep = .Platform$file.sep), header = TRUE, row.names = 1)[1, 1:10] ## ----echo=FALSE--------------------------------------------------------------- read.table(paste(DATADIR, "gxe.txt", sep = .Platform$file.sep), header = TRUE, row.names = 1)[1:2, 1:10] ## ----echo = FALSE------------------------------------------------------------- read.table(paste(DATADIR, "methylation.txt", sep = .Platform$file.sep), header = TRUE)[1:5, 1:7] ## ----echo = FALSE------------------------------------------------------------- read.table(paste(DATADIR, "snp.txt", sep = .Platform$file.sep), header = TRUE)[1:5, 1:15] ## ----eval=TRUE, fig.width=6, fig.height=6, out.width=600, out.height=600------ env_file_name = paste(DATADIR, "env.txt", sep = .Platform$file.sep) covariate_file_name = paste(DATADIR, "cov.txt", sep = .Platform$file.sep) methylation_file_name = paste(DATADIR, "methylation.txt", sep = .Platform$file.sep) Emodel_pv = 1 Emodel_result_file_name = "Result_Emodel.txt" Emodel_qqplot_file_name = "QQplot_Emodel.jpg" GEM_Emodel(env_file_name, covariate_file_name, methylation_file_name, Emodel_pv, Emodel_result_file_name, Emodel_qqplot_file_name, savePlot=FALSE) ## ----echo=FALSE--------------------------------------------------------------- head(read.table(paste(getwd(), "Result_Emodel.txt", sep = .Platform$file.sep), header = TRUE)) ## ----eval=TRUE---------------------------------------------------------------- snp_file_name = paste(DATADIR, "snp.txt", sep = .Platform$file.sep) covariate_file_name = paste(DATADIR, "cov.txt", sep = .Platform$file.sep) methylation_file_name = paste(DATADIR, "methylation.txt", sep = .Platform$file.sep) Gmodel_pv = 1e-04 Gmodel_result_file_name = "Result_Gmodel.txt" GEM_Gmodel(snp_file_name, covariate_file_name, methylation_file_name, Gmodel_pv, Gmodel_result_file_name) ## ----echo=FALSE--------------------------------------------------------------- head(read.table(paste(getwd(), "Result_Gmodel.txt", sep = .Platform$file.sep), header = TRUE)) ## ----eval=TRUE, fig.keep='all', dev='png', fig.width=8, fig.height=5, out.width=600, out.height=400---- snp_file_name = paste(DATADIR, "snp.txt", sep = .Platform$file.sep) covariate_file_name = paste(DATADIR, "gxe.txt", sep = .Platform$file.sep) methylation_file_name = paste(DATADIR, "methylation.txt", sep = .Platform$file.sep) GxEmodel_pv = 1 GxEmodel_result_file_name = "Result_GxEmodel.txt" GEM_GxEmodel(snp_file_name, covariate_file_name, methylation_file_name, GxEmodel_pv, GxEmodel_result_file_name, topKplot = 1, savePlot=FALSE) ## ----echo=FALSE--------------------------------------------------------------- head(read.table(paste(getwd(), "Result_GxEmodel.txt", sep = .Platform$file.sep), header = TRUE))