MnM.test {methylMnM} | R Documentation |
The function is used to compute p-value of each bin.
MnM.test(file.dataset=NULL,chrstring=NULL,file.cpgbin=NULL, file.mrecpgbin=NULL,writefile=NULL,reportfile=NULL, mreratio=3/7,method="XXYY", psd=2,mkadded=1,a=1e-16, cut=100,top=500)
file.dataset |
The files path of sample. (datafile should be c(datafile1,datafile2,datafile3,datafile4), where datafile1 and datafile2 are path of Medip-seq data, datafile3 and datafile4 are path of MRE-seq data). |
chrstring |
The chromosome should be test. |
file.cpgbin |
The file path of all CpG number of each bin. |
file.mrecpgbin |
The file path of MRE-CpG number of each window (If NULL, mrecpgfile will equal to cpgfile). |
writefile |
The file path of output result. (If writefile=NULL, there will return the results back to main program ) |
reportfile |
The path of output results of bin length, 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). |
method |
Option different data for the test. |
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) |
a |
Cut-off for recalculating p-value with multinomial distribution when normal p-values smaller than a and the sum of observations smaller than top. |
cut |
Cut-off for recalculating p-value with multinomial distribution when the sum of observations smaller than cut. |
top |
Cut-off for recalculating p-value with multinomial distribution when normal p-values smaller than a and the sum of observations smaller than top. |
The output file "writefile" will own eleven columns, that is, "chr", "chrSt", "chrEnd", "Medip1", "Medip2", "MRE1", "MRE2", "cg", "mrecg", "pvalue" and "plus-minus". 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".
Yan Zhou, Bo Zhang, Nan Lin, BaoXue Zhang and Ting Wang
datafile<-system.file("extdata", package = "methylMnM") filepath<-datafile[1] file1<-paste(filepath,"/all_CpGsite_chr18.txt",sep="") CpGsite<-read.table(file1, header=FALSE,skip=0, nrows=200, as.is=TRUE) winbin<-CpGsite[1:100,1:4] winbin[,2]<-seq(0,49500,500) winbin[,3]<-winbin[,2]+500 winbin[,4]<-rpois(100, lambda=5) winbinfile1<-paste(setwd(getwd()), "/winbinfile1.bed", sep = "") write.table(winbin, winbinfile1,sep="\t", quote=FALSE, row.names =FALSE) winbin1<-winbin winbin1[,4]<-winbin[,4]+20 winbinfile2<-paste(setwd(getwd()), "/winbinfile2.bed", sep = "") write.table(winbin1, winbinfile2,sep="\t", quote=FALSE, row.names =FALSE) datafile<-c(winbinfile1,winbinfile2) cpg<-winbin cpg[,4]<-rpois(100, lambda=12) cpgfile<-paste(setwd(getwd()), "/cpgfile.bed", sep = "") write.table(cpg, cpgfile, sep="\t", quote=FALSE, row.names =FALSE) f<-MnM.test(file.dataset=datafile,file.cpgbin=cpgfile)