methylMnM (version 1.10.0)

CNVnormal: Normalize copy number variation (CNV).

Description

The function is used to normalize copy number variation.

Usage

CNVnormal(CNVfile,bincount)

Arguments

CNVfile

The path of copy number variation file.

bincount

Count of all bins.

Value

Count of all bins after CNV normalization.

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)