CNVnormal {methylMnM} | R Documentation

## 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.

### 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)

[Package methylMnM version 1.28.0 Index]