Description Usage Arguments Value Author(s) Examples

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

1 2 3 4 |

`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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
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)
``` |

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