removeblacklist {methylMnM} | R Documentation

## Remove blacklist.

### Description

The function is used to remove blacklist which we are not interest.

### Usage

    removeblacklist(file2,cpg)

### Arguments

`file2` | The path of blacklist site file.
`cpg` | All bins.

### Value

All bins except blacklist region.

### Author(s)

Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang

### Examples

      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)

[Package methylMnM version 1.25.0 Index]