countMREcpgbin {methylMnM} | R Documentation

## Compute the MRE CpG number of each bin with MRE CpG sites.

### Description

The function is used to compute the MRE CpG number of each bin with MRE CpG sites. MRE CpG is some specific CpGs in genome-wide, such as "CCGG", "GCGC" and "CCGC". The specific CpG number is directly bound up with each experiment.

### Usage

    countMREcpgbin(mrecpg.site,file.allcpgsite,file.bin=NULL,
    writefile=NULL, binlength=500)

### Arguments

`mrecpg.site` | The data of mreCpG site.
`file.allcpgsite` | The path of all cpg site file or sequence tag file.
`file.bin` | The path of all bins file. For computing the number of sequence tag of each window, we use the file as a normalize window position. (If we do not use the file, there will be defaulted as NULL).
`writefile` | The path of output result. (If writefile=NULL, there will return the results back to main program )
`binlength` | The length of each window. (Defaulted length is 500)

### Value

The output file is include four columns, that is "chromosome", "start position", "end position" and "MRE CpG count".

### Author(s)

Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang

### Examples

      datafile<-system.file("extdata",  package = "methylMnM")
      filepath<-datafile[1]
      file<-paste(filepath,"/three_Mre_CpGsite_chr18.txt",sep="")
      file1<-paste(filepath,"/all_CpGsite_chr18.txt",sep="")
      five_Mre_CpGsite<-read.table(file, header=FALSE, as.is=TRUE)
      f<-countMREcpgbin(mrecpg.site=five_Mre_CpGsite[1:1000,],
    file.allcpgsite=file1,binlength=5000)

[Package methylMnM version 1.28.0 Index]