MnM.test {methylMnM} | R Documentation

## Compute p-value of each bin.

### Description

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

### Usage

    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)

### Arguments

`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.

### Value

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".

### 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)
      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)

[Package methylMnM version 1.25.0 Index]