MnM.selectDMR {methylMnM} | R Documentation |
The function is used to select significants of each comparation.
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)
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. |
The DMRs of the comparation.
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
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")