countMREbin: Compute the total MRE-seq number of each bin.
In methylMnM: detect different methylation level (DMR)

Description Usage Arguments Value Author(s) Examples

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

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

`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).

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.

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

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