MnM.qvalue {methylMnM} | R Documentation

## Estimate the q-values for a given set of p-values

### Description

The function is used to estimate the q-values for a given set of p-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.

### Usage

    MnM.qvalue(datafile,writefile=NULL,reportfile=NULL)

### Arguments

`datafile` | Input data of p-values file (Including all input)
`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.

### Value

The output file is just add a q-value column to the input file.

### 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')
      pvaluefile<-paste(setwd(getwd()), "/pvalue.bed", sep = "")
      write.table(cpgpq, pvaluefile,sep="\t", quote=FALSE,row.names =FALSE)
      f<-MnM.qvalue(datafile=pvaluefile)

[Package methylMnM version 1.28.0 Index]