MnM.qvalue {methylMnM} | R Documentation |
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.
MnM.qvalue(datafile,writefile=NULL,reportfile=NULL)
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. |
The output file is just add a q-value column to the input file.
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') pvaluefile<-paste(setwd(getwd()), "/pvalue.bed", sep = "") write.table(cpgpq, pvaluefile,sep="\t", quote=FALSE,row.names =FALSE) f<-MnM.qvalue(datafile=pvaluefile)