Description Usage Arguments Value Author(s) Examples

View source: R/MnM.selectDMR.R

The function is used to select significants of each comparation.

1 2 3 | ```
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

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

```
Loading required package: edgeR
Loading required package: limma
Loading required package: statmod
[1] Total number of frames: 100
[1] Remaining number of frames with MRE-CpG=0 and p.value<=0.1: 0
[1] Remaining number of frames with MRE-CpG!=0 and p.value<=0.1: 12
[1] Remaining number of frames with D_value>=2& CpG!=0: 8
[1] Remaining number of frames with ratio<=0.689655172413793 or ratio>=1.45: 6
[1] [Note: There are 0 frames associated to a p-value==0.]
[1] Remaining number of frames called DMR:6
```

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