countMREbin {methylMnM} | R Documentation

## Compute the total MRE-seq number of each bin.

### Description

The function is used to compute the total MRE-seq number of each bin.

### Usage

    countMREbin(file.MREsite,file.blacklist=NULL, file.bin=NULL,
    file.CNV=NULL, cutoff=0,writefile=NULL,
    reportfile=NULL, binlength=500)

### Arguments

`file.MREsite` | The path of MRE-seq sites file.
`file.blacklist` | The path of blacklist file (If we do not use the file, there will be defaulted as NULL).
`file.bin` | The path of all bin file. For computing the number of sequence tag of each window, we use the file as a normalization window position. (If we do not use the file, there will be defaulted as NULL).
`file.CNV` | If need, we should input CNV file to normalize count of each bin.
`cutoff` | The critical value of PCR. (If we do not use the critical value, there will be defaulted as 0.)
`writefile` | The path of output results. (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.
`binlength` | The length of each window.(Defaulted length is 500).

### Value

The MRE-seq sites should include at least three columns "chromosome", "start position" and "end position". The output file is include four columns, that is "chromosome", "start position", "end position" and "MRE-seq count". Also, the function output a report for some parameters.

### Author(s)

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

### Examples

      datafile<-system.file("extdata",  package = "methylMnM")
      filepath<-datafile[1]
      file.MREsite<-paste(filepath,"/all_CpGsite_chr18.txt",sep="")
      f<-countMREbin(file.MREsite, binlength=5000)

[Package methylMnM version 1.20.0 Index]