MnM.selectDMR {methylMnM} | R Documentation

## Select significants of each comparation.

### Description

The function is used to select significants of each comparation.

### Usage

    MnM.selectDMR(frames = NULL, up =1.45, down = 1/1.45, p.value.MM = 0.01,
     p.value.SAGE = 0.01,q.value = 0.01,cutoff="q-value",  quant= 0.6)

### Arguments

`frames` | The input dataset and q-values of each bin.
`up` | The ratio of Medip1/Medip2 should be larger than "up" value if we call it significant.
`down` | The ratio of Medip1/Medip2 should be smaller than "down" value if we call it significant.
`p.value.MM` | The p-value of the bin which use MM test should be smaller than "p.value.MM" if we call it significant.
`p.value.SAGE` | The p-value of the bin which use SAGE test should be smaller than "p.value.SAGE" if we call it significant.
`q.value` | The q-value of the bin should be smaller than "q.value" if we call it significant.
`cutoff` | We should use p-value or q-value cutoff to detect DMRs (If cutoff="q-value", then we use q-value to detect DMRs, else we use p-value ).
`quant` | The rank of absolute value of (Medip1-Medip2) should be larger than "quant" value if we call it significant.

### Value

The DMRs of the comparation.

### 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
      count<-matrix(rpois(600, lambda=5), nrow=100 )
      count[,6]<-count[,5]
      pvalue<-runif(100, min=0, max=1)
      ts<-rnorm(100, mean=0, sd=1)
      cpgpq<-cbind(winbin[,1:3],count,pvalue,ts)
      colnames(cpgpq)=c("chr", "chrSt","chrEnd","Medip1","Medip2","MRE1",
      "MRE2","cg","mrecg","pvalue",'Ts')
      f<-MnM.selectDMR(frames=cpgpq, p.value.MM = 0.1,
      p.value.SAGE = 0.1,cutoff="p-value")

[Package methylMnM version 1.28.0 Index]