2015-7-10-001-code
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# shared high HDRC regions based on normal samples setwd("/home/sguo/methylation") file=list.files(pattern="*mh.cor.RData") load(file[i]) cancer=substr(file[1],1,4) edge=0.6 newcor<-cor[which(cor[,2]>edge),] bed1<-cor2bed(rownames(newcor)) print(nrow(bed1)) number<-c() region<-c(rownames(newcor)) for(i in 2:length(file)){ load(file[i]) cancer=substr(file[i],1,4) newcor<-cor[which(cor[,2]>edge),] bed2<-cor2bed(rownames(newcor)) bed1<-Rbedtools(functionstring="intersectBed",bed1,bed2,opt.string="-wa") ntmp<-c(nrow(bed1),nrow(bed2)) number<-c(number,nrow(bed1)) region<-c(region,rownames(newcor)) } regionx1<-unique(region) regionx2<-cor2bed(regionx1) write.table(regionx1,file="conservative.methylation.block.0.6.normal.cor",sep="\t",col.names=F,row.names=F,quote=F) write.table(regionx2,file="conservative.methylation.block.0.6.normal.bed",sep="\t",col.names=F,row.names=F,quote=F) write.table(bed1,file="conservative.methylation.block.C11.0.6.normal.bed",sep="\t",col.names=F,row.names=F,quote=F)