Description Usage Arguments Value Author(s) Examples

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.

1 | ```
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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
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)
``` |

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