CNVnormal {methylMnM} | R Documentation |
The function is used to normalize copy number variation.
CNVnormal(CNVfile,bincount)
CNVfile |
The path of copy number variation file. |
bincount |
Count of all bins. |
Count of all bins after CNV normalization.
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
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)