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 1.30.0 Index]