EMtest: Inferring the methylation expression level of single sites.

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

Description

Using statistical framework and EM algorithm to infer the methylation expression level of single sites.

Usage

EMtest(datafile = NULL, chrstring = NULL, cpgfile, mrecpgfile = NULL,
  writefile = NULL, reportfile = NULL, mreratio = 3/7, psd = 2,
  mkadded = 1, f = 1)

Arguments

datafile	The files of sample. (datafile should be cbind(data1,data2, data3,data4), where data1 and data2 are Medip-seq data, data3 and data4 are MRE-seq data).
chrstring	The chromosome should be test.
cpgfile	The file of all CpG number.
mrecpgfile	The file of MRE-CpG number(If NULL, mrecpgfile will equal to cpgfile).
writefile	The path of file of output result. (If writefile=NULL, there will return the results back to main program)
reportfile	The path of output results of the number of bin, total reads before processing and total reads after processing.
mreratio	The ratio of total unmethylation level with total methylation level (Defaulted mreratio is 3/7).
psd	The parameters of pseudo count, which pseudo count added to Medip-seq and MRE-seq count.
mkadded	Added to all CpG and MRE CpG (We set psd=2 and mkadded=1 as defaulted for robust).
f	Adjustment weight, default to 1.

Value

values or file The output file "writefile" will own eleven columns, that is, "chr", "chrSt", "chrEnd", "Medip1", "Medip2", "MRE1", "MRE2", "cg","mrecg","pvalue" and "Ts". We also output a report file which will include parameters "s1/s2", "s3/s4", "N1", "N2", "N3", "N4", "c1", "c2", "Number of windows" and "Spend time".

Examples

data(example_data)
data1 <- EM2_H1ESB1_MeDIP_sigleCpG
data2 <- EM2_H1ESB2_MeDIP_sigleCpG
data3 <- H1ESB1_MRE_sigleCpG
data4 <- H1ESB2_MRE_sigleCpG
datafile <- cbind(data1, data2, data3, data4)
allcpg <- all_CpGsite_bin_chr18
mrecpg <- three_mre_cpg
dirwrite <- paste(setwd(getwd()), "/", sep="")
writefile <- paste(dirwrite, "pval_EM_H1ESB1_H1ESB21.bed", sep="")
reportfile <- paste(dirwrite, "report_pvalH1ESB1_H1ESB21.bed", sep="")
EMtest(datafile=datafile, chrstring=NULL, cpgfile=allcpg,
       mrecpgfile=mrecpg, writefile=writefile, reportfile=reportfile,
       mreratio=3/7, psd=2, mkadded=1, f=1)

SIMD documentation built on Nov. 8, 2020, 5:12 p.m.