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2
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1 #!/usr/bin/env Rscript
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2 args <- commandArgs(trailingOnly = TRUE)
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3 fileR=args[1]
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4 fileT=args[2]
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5 #ofile=args[3]
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6 data_R=read.table(fileR,header=T)
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7 data_T=read.table(fileT,header=T)
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8
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9 #P=wilcox.test(data_R$Score,data_T$Score,alternative="gr")$p.value
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10 range= rev(seq(min(data_R$VINYL_score),max(data_R$VINYL_score),0.5))
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11 #header=paste("Cut-off","PosD","PosH","FisherPV","OR",sep="\t");
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12 #cat(header,file=ofile,sep="\n",append=T)
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13
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14 m=matrix(ncol=2,nrow=2)
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15 totR=nrow(data_R)
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16 totT=nrow(data_T)
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17 FoddsB=1;
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18 FpvalB=1;
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19 Fstring="";
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20 for (r in range)
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21 {
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22 posR=sum(data_R$VINYL_score>=r);
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23 posT=sum(data_T$VINYL_score>=r);
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24 m[,1]=c(posR,totR);
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25 m[,2]=c(posT,totT);
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26
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27 F=fisher.test(m,alternative="greater")
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28 Fpv=F$p.value
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29 Fodds=F$estimate
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30
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31 string=paste(r,posR,posT,Fpv,Fodds,sep="\t")
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32 if (Fpv<= FpvalB && Fodds!=Inf && Fodds>=4 && Fodds>FoddsB)
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33 {
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34 FoddsB= Fodds
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35 FpvalB= Fpv
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36 Fstring= string
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37 }
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38 }
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39
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40 cat(Fstring)
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