## ----eval=FALSE--------------------------------------------------------------- # install.packages("BiocManager") # BiocManager::install(c('edgeR', 'statmod','methylMnM')) # # library(edgeR) # library(statmod) # library(methylMnM) ## ----eval=FALSE--------------------------------------------------------------- # BiocManager::install("SIMD") ## ----------------------------------------------------------------------------- library(SIMD) ## ----------------------------------------------------------------------------- datafile <- system.file("extdata", package="methylMnM") filepath <- datafile[1] ## ----------------------------------------------------------------------------- dirwrite <- paste(setwd(getwd()), "/", sep="") ## ----------------------------------------------------------------------------- data(example_data) allcpgfile <- EM_H1ESB1_MeDIP_sigleCpG readshort <- paste(filepath, "/H1ESB1_MeDIP_18.extended.txt", sep="") writefile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG.bed", sep="") reportfile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG_report.bed", sep="") EMalgorithm(cpgsitefile=readshort, allcpgfile=allcpgfile, category="1", writefile=writefile, reportfile=reportfile) ## ----------------------------------------------------------------------------- data(example_data) data1 <- EM2_H1ESB1_MeDIP_sigleCpG data2 <- EM2_H1ESB2_MeDIP_sigleCpG data3 <- H1ESB1_MRE_sigleCpG data4 <- H1ESB2_MRE_sigleCpG datafile <- cbind(data1,data2,data3,data4) allcpg <- all_CpGsite_bin_chr18 mrecpg <- three_mre_cpg dirwrite <-paste(setwd(getwd()), "/", sep="") writefile <- paste(dirwrite, "pval_EM_H1ESB1_H1ESB21.bed", sep="") reportfile <- paste(dirwrite, "report_pvalH1ESB1_H1ESB21.bed", sep="") EMtest(datafile=datafile, chrstring=NULL, cpgfile=allcpg,mrecpgfile=mrecpg, writefile=writefile, reportfile=reportfile,mreratio=3/7, psd=2, mkadded=1, f=1)