methylMnM (version 1.10.0)

countMREbin: 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.

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)