EMalgorithm: EM algorithm to infer CpG sites.

In FocusPaka/SIMD: Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

Description

Using EM algorithm to infer the real number of CpG sites.

Usage

EMalgorithm(cpgsitefile, allcpgfile, category = "1", writefile = NULL,
  reportfile = NULL)

Arguments

cpgsitefile	The path of file to store CpG site.
allcpgfile	The file to store CpG sites.
category	Default to "1".
writefile	The path of output results. (If writefile=NULL, there will return the results back to main program.)
reportfile	The path of output results.

Value

values or file If writefile is NULL, then return the values of results,otherwise output to write file.

Examples

datafile <- system.file("extdata", package="methylMnM")
data(example_data)
filepath <- datafile[1]
allcpgfile <- EM_H1ESB1_MeDIP_sigleCpG
dirwrite <- paste(setwd(getwd()), "/", sep="")
readshort <- paste(filepath, "/H1ESB1_MeDIP_18.extended.txt", sep="")
writefile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG.bed", sep="")
reportfile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG_report.bed", sep="")
f <- EMalgorithm(cpgsitefile=readshort, allcpgfile=allcpgfile, category="1",
                 writefile=writefile, reportfile=reportfile)

FocusPaka/SIMD documentation built on May 29, 2019, 10:57 a.m.