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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$VINYL_score),0.5))
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11 header=paste("Cut-off","PosD","PosH","FisherPV","OR",sep="\t");
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12 cat(header,file=ofile,sep="\n",append=T)
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13
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14 m=matrix(ncol=2,nrow=2)
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15 totR=nrow(data_R)
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16 totT=nrow(data_T)
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17 for (r in range)
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18 {
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19 posR=sum(data_R$VINYL_score>=r);
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20 posT=sum(data_T$VINYL_score>=r);
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21 m[,1]=c(posR,totR);
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22 m[,2]=c(posT,totT);
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23
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24 F=fisher.test(m,alternative="greater")
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25 Fpv=F$p.value
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26 Fodds=F$estimate
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27
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28 string=paste(r,posR,posT,Fpv,Fodds,sep="\t")
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29 cat(string,file=ofile,sep="\n",append=T)
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30 }
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