Description Usage Arguments Value Examples
Using statistical framework and EM algorithm to infer the methylation expression level of single sites.
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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. |
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".
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
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