CNVnormal: Normalize copy number variation (CNV).

In methylMnM: detect different methylation level (DMR)

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)

Example output

sh: 1: cannot create /dev/null: Permission denied
Loading required package: edgeR
Loading required package: limma
Loading required package: statmod
Doing CNV normalization

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