methylMnM (version 1.10.0)

MnM.test: 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".

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)