removeblacklist {methylMnM} | R Documentation |
The function is used to remove blacklist which we are not interest.
removeblacklist(file2,cpg)
file2 |
The path of blacklist site file. |
cpg |
All bins. |
All bins except blacklist region.
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
datafile<-system.file("extdata", package = "methylMnM") filepath<-datafile[1] file1<-paste(filepath,"/all_CpGsite_chr18.txt",sep="") CpGsite<-read.table(file1, header=FALSE,skip=0, nrows=200, as.is=TRUE) winbin<-CpGsite[1:100,1:4] winbin[,2]<-seq(0,49500,500) winbin[,3]<-winbin[,2]+500 winbin[,4]<-rpois(100, lambda=5) blacklist<-winbin[1:5,] blacklist[,2]<-c(0,10000,20000,30000,40000) blacklist[,3]<-blacklist[,2]+1000 blacklistfile<-paste(setwd(getwd()), "/blacklist.bed", sep = "") write.table(blacklist, blacklistfile, quote=FALSE, row.names =FALSE,col.names =FALSE) f<-removeblacklist(blacklistfile,winbin)