Normalize copy number variation (CNV).

Description

The function is used to normalize copy number variation.

Usage

CNVnormal(CNVfile,bincount)

Arguments

Value

Count of all bins after CNV normalization.

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)
  cnv<-winbin[1:5,]
  cnv[,2]<-c(0,10000,20000,30000,40000)
  cnv[,3]<-cnv[,2]+10000
  cnv[,4]<-c(1.2,1.6,1,2,1)
  CNVfile<-paste(setwd(getwd()), "/CNVfile.bed", sep = "")  
  write.table(cnv, CNVfile, quote=FALSE, row.names =FALSE,col.names =FALSE)
  f<-CNVnormal(CNVfile,winbin)