methylMnM (version 1.10.0)

removeblacklist: 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.

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)