removeblacklist: Remove blacklist.

In methylMnM: detect different methylation level (DMR)

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)

methylMnM documentation built on Nov. 8, 2020, 6:47 p.m.