## ----------------------------------------------------------------------------------------------------------------------- # install.packages("BiocManager") # BiocManager::install(c('edgeR', 'statmod','methylMnM')）＃＃library（edger）＃library（statmod）＃library（甲基mnm）## --------------------------------------------------------------------------------------------------------------------------------------------＃Biocmanager :: install（“ simd”）##----------------------------------------------------------------------------------------------------------------------库（SIMD）## -------------------------------------------------------------------------------------------------------------------------------------------------数据文件<-System.File（“ Extdata”，package =“ ethylmnm”）filepath <-datafile [1] ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- dirwrite <- paste(setwd(getwd()), "/", sep="") ## -------------------------------------------------------------------------------------------------------------------数据（example_data）allcpgfile <-em_h1esb1_medip_medip_siglecpg readShort <-paste（filepath，“/h1esb1_medip_18.extended.txt”，sep =“”，sep =“”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) ## ---------------------------------------------------------------------------------------------------------------------数据（example_data）数据1 <-em2_h1esb1_medip_siglecpg data2 <-em2_h1esb2_medip_medip_siglecpg data3 <-h1esb1_mre_siglecpg data4（Data1，data2，data3，data4）allcpg <-all_cpgsite_bin_chr18 mrecpg <-try_mre_cpg dirwrite <-paste <-paste（setWd（getwd（getwd（）），“/”/“”，sep =“”，sep =“”）writefile <-paste <-paste（dirwrite，dirwrite，dirwrite，dirwrite，dirwrite，“, 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）