EMalgorithm {SIMD}R Documentation

EM algorithm to infer CpG sites.

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)

[Package SIMD version 1.12.0 Index]