### R code from vignette source 'methylMnM.Rnw' ################################################### ### code chunk number 1: methylMnM.Rnw:63-69 (eval = FALSE) ################################################### ## if (!requireNamespace("BiocManager", quietly=TRUE)) ## install.packages("BiocManager") ## BiocManager::install("edgeR") ## BiocManager::install("statmod") ## library(edgeR) ## library(statmod) ################################################### ### code chunk number 2: methylMnM.Rnw:75-78 (eval = FALSE) ################################################### ## if (!requireNamespace("BiocManager", quietly=TRUE)) ## install.packages("BiocManager") ## BiocManager::install("methylMnM") ################################################### ### code chunk number 3: methylMnM.Rnw:82-83 ################################################### library(methylMnM) ################################################### ### code chunk number 4: methylMnM.Rnw:165-167 ################################################### datafile<-system.file("extdata", package = "methylMnM") filepath<-datafile[1] ################################################### ### code chunk number 5: methylMnM.Rnw:174-175 ################################################### dirwrite<-paste(setwd(getwd()),"/",sep="") ################################################### ### code chunk number 6: methylMnM.Rnw:189-195 ################################################### binlength<-500 file.cpgsite<-paste(filepath,"/all_CpGsite_chr18.txt",sep="") writefile<-paste(dirwrite,"numallcpg.bed",sep="") reportfile<-paste(dirwrite,"report_numallcpg.txt",sep="") countcpgbin(file.cpgsite,file.blacklist=NULL,file.bin=NULL, writefile=writefile, reportfile=reportfile, binlength=binlength) ################################################### ### code chunk number 7: methylMnM.Rnw:234-244 ################################################### file<-paste(filepath,"/three_Mre_CpGsite_chr18.txt",sep="") file1<-paste(filepath,"/all_CpGsite_chr18.txt",sep="") allcpgfile<-paste(dirwrite,"numallcpg.bed",sep="") five_Mre_CpGsite<-read.table(file, header=FALSE, as.is=TRUE) four_Mre_CpGsite<-five_Mre_CpGsite[five_Mre_CpGsite[,4]!="ACGT",] mrecpg.site<-four_Mre_CpGsite[four_Mre_CpGsite[,4]!="CGCG",] writefile<-paste(dirwrite,"three_mre_cpg.bed",sep="") countMREcpgbin(mrecpg.site,file.allcpgsite=file1,file.bin=allcpgfile,writefile=writefile, binlength=500) ################################################### ### code chunk number 8: methylMnM.Rnw:276-282 ################################################### file3<-paste(filepath,"/H1ESB1_MeDIP_18.extended.txt",sep="") allcpgfile<-paste(dirwrite,"numallcpg.bed",sep="") writefile<-paste(dirwrite,"H1ESB1_MeDIP_num500_chr18.bed",sep="") reportfile<-paste(dirwrite,"H1ESB1_MeDIP_num500_chr18_report.txt",sep="") countMeDIPbin(file.Medipsite=file3,file.blacklist=NULL,file.bin=allcpgfile,file.CNV=NULL,writefile=writefile, reportfile=reportfile, binlength=500) ################################################### ### code chunk number 9: methylMnM.Rnw:316-321 ################################################### file4<-paste(filepath,"/H1ESB1_MRE_18.extended.txt",sep="") writefile<-paste(dirwrite,"H1ESB1_MRE_num500_chr18.bed",sep="") reportfile<-paste(dirwrite,"H1ESB1_MRE_num500_chr18_report.bed",sep="") countMREbin(file.MREsite=file4,file.blacklist=NULL, file.bin=allcpgfile,file.CNV=NULL, cutoff=0.05,writefile=writefile, reportfile=reportfile, binlength=500) ################################################### ### code chunk number 10: methylMnM.Rnw:356-362 ################################################### file5<-paste(filepath,"/H1ESB2_Medip_18.extended.txt",sep="") allcpgfile<-paste(dirwrite,"numallcpg.bed",sep="") writefile<-paste(dirwrite,"H1ESB2_MeDIP_num500_chr18.bed",sep="") reportfile<-paste(dirwrite,"H1ESB2_MeDIP_num500_chr18_report.txt",sep="") countMeDIPbin(file.Medipsite=file5,file.blacklist=NULL,file.bin=allcpgfile,file.CNV=NULL,writefile=writefile, reportfile=reportfile, binlength=500) ################################################### ### code chunk number 11: methylMnM.Rnw:367-372 ################################################### file6<-paste(filepath,"/H1ESB2_MRE_18.extended.txt",sep="") writefile<-paste(dirwrite,"H1ESB2_MRE_num500_chr18.bed",sep="") reportfile<-paste(dirwrite,"H1ESB2_MRE_num500_chr18_report.txt",sep="") countMREbin(file.MREsite=file6,file.blacklist=NULL, file.bin=allcpgfile,file.CNV=NULL, cutoff=0.05,writefile=writefile, reportfile=reportfile, binlength=500) ################################################### ### code chunk number 12: methylMnM.Rnw:391-403 ################################################### datafile1<-paste(dirwrite,"H1ESB1_MeDIP_num500_chr18.bed",sep="") datafile2<-paste(dirwrite,"H1ESB2_MeDIP_num500_chr18.bed",sep="") datafile3<-paste(dirwrite,"H1ESB1_MRE_num500_chr18.bed",sep="") datafile4<-paste(dirwrite,"H1ESB2_MRE_num500_chr18.bed",sep="") datafile<-c(datafile1,datafile2,datafile3,datafile4) chrstring<-NULL cpgfile<-paste(dirwrite,"numallcpg.bed",sep="") mrecpgfile<-paste(dirwrite,"three_mre_cpg.bed",sep="") writefile<-paste(dirwrite,"pvalH1ESB1_H1ESB2_chr18.bed",sep="") reportfile<-paste(dirwrite,"report_pvalH1ESB1_H1ESB2_chr18.txt",sep="") MnM.test(file.dataset=datafile,chrstring=chrstring,file.cpgbin=cpgfile,file.mrecpgbin=mrecpgfile,writefile=writefile,reportfile=reportfile,mreratio=3/7,method="XXYY", psd=2,mkadded=1,a=1e-16,cut=100,top=500) ################################################### ### code chunk number 13: methylMnM.Rnw:459-464 ################################################### datafile<-paste(dirwrite,"pvalH1ESB1_H1ESB2_chr18.bed",sep="") writefile<-paste(dirwrite,"q_H1ESB1_H1ESB2_chr18.bed",sep="") reportfile<-paste(dirwrite,"report_q_H1ESB1_H1ESB2_chr18.bed",sep="") MnM.qvalue(datafile,writefile,reportfile) ################################################### ### code chunk number 14: methylMnM.Rnw:489-494 ################################################### file<-paste(dirwrite,"q_H1ESB1_H1ESB2_chr18.bed",sep="") frames<-read.table(file, header=TRUE,sep="\t", as.is=TRUE) DMR<-MnM.selectDMR(frames =frames , up = 1.45, down =1/1.45, p.value.MM = 0.01, p.value.SAGE = 0.01,q.value =0.01,cutoff="q-value", quant= 0.6) writefile<-paste(dirwrite,"DMR_e5_H1ESB1_H1ESB2_chr18.bed",sep="") write.table(DMR, writefile,sep="\t", quote=FALSE,row.names=FALSE)