countMREcpgbin: Compute the MRE CpG number of each bin with MRE CpG sites.

In methylMnM: detect different methylation level (DMR)

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)

Example output

Loading required package: edgeR
Loading required package: limma
Loading required package: statmod
Count MRE-CpG number of each window
Reading data, please wait...
Obtaining CpG sites which are included in MRE-CpG sites.
0
Count MRE-CpG number of each window of chr18
0
[1] 1

methylMnM documentation built on Nov. 8, 2020, 6:47 p.m.