methylMnM (version 1.10.0)

countMREcpgbin: 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".

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)