MnM.test: Compute p-value of each bin.
In methylMnM: detect different methylation level (DMR)

Description Usage Arguments Value Author(s) Examples

The function is used to compute p-value of each bin.

MnM.test(file.dataset=NULL,chrstring=NULL,file.cpgbin=NULL,
file.mrecpgbin=NULL,writefile=NULL,reportfile=NULL,
mreratio=3/7,method="XXYY", psd=2,mkadded=1,a=1e-16,
cut=100,top=500)

`file.dataset`	The files path of sample. (datafile should be c(datafile1,datafile2,datafile3,datafile4), where datafile1 and datafile2 are path of Medip-seq data, datafile3 and datafile4 are path of MRE-seq data).
`chrstring`	The chromosome should be test.
`file.cpgbin`	The file path of all CpG number of each bin.
`file.mrecpgbin`	The file path of MRE-CpG number of each window (If NULL, mrecpgfile will equal to cpgfile).
`writefile`	The file path of output result. (If writefile=NULL, there will return the results back to main program )
`reportfile`	The path of output results of bin length, the number of bin, total reads before processing and total reads after processing.
`mreratio`	The ratio of total unmethylation level with total methylation level (Defaulted mreratio is 3/7).
`method`	Option different data for the test.
`psd`	The parameters of pseudo count, which pseudo count added to Medip-seq and MRE-seq count.
`mkadded`	Added to all CpG and MRE CpG (We set psd=2 and mkadded=1 as defaulted for robust)
`a`	Cut-off for recalculating p-value with multinomial distribution when normal p-values smaller than a and the sum of observations smaller than top.
`cut`	Cut-off for recalculating p-value with multinomial distribution when the sum of observations smaller than cut.
`top`	Cut-off for recalculating p-value with multinomial distribution when normal p-values smaller than a and the sum of observations smaller than top.

The output file "writefile" will own eleven columns, that is, "chr", "chrSt", "chrEnd", "Medip1", "Medip2", "MRE1", "MRE2", "cg", "mrecg", "pvalue" and "plus-minus". We also output a report file which will include parameters "s1/s2", "s3/s4", "N1", "N2", "N3", "N4", "c1", "c2", "Number of windows" and "Spend time".

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)
  winbinfile1<-paste(setwd(getwd()), "/winbinfile1.bed", sep = "")  
  write.table(winbin, winbinfile1,sep="\t", quote=FALSE, row.names =FALSE)
  winbin1<-winbin
  winbin1[,4]<-winbin[,4]+20
  winbinfile2<-paste(setwd(getwd()), "/winbinfile2.bed", sep = "")  
  write.table(winbin1, winbinfile2,sep="\t", quote=FALSE, row.names =FALSE)
  datafile<-c(winbinfile1,winbinfile2)
  cpg<-winbin
  cpg[,4]<-rpois(100, lambda=12)
  cpgfile<-paste(setwd(getwd()), "/cpgfile.bed", sep = "")  
  write.table(cpg, cpgfile, sep="\t", quote=FALSE, row.names =FALSE)
  f<-MnM.test(file.dataset=datafile,file.cpgbin=cpgfile)