EMalgorithm {SIMD} | R Documentation |
Using EM algorithm to infer the real number of CpG sites.
EMalgorithm(cpgsitefile, allcpgfile, category = "1", writefile = NULL, reportfile = NULL)
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. |
values or file If writefile is NULL, then return the values of results,otherwise output to write file.
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)