A script to create files in ABSOLUTE FORMAT

cat FREEC_ratio2Absolute.R | R --slave --args <*_ratio.txt>

Author: valeu

scripts/FREEC_ratio2Absolute.R

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+args <- commandArgs()
+
+#read _ratio.txt:
+dataTable <-read.table(args[4], header=TRUE);
+
+ratio<-data.frame(dataTable)
+
+cat ("Chromosome\tStart\tEnd\tNum_Probes\tSegment_Mean")
+
+weirdNum=345
+
+for (i in c(unique(dataTable$Chromosome))) {
+	tt <- which(ratio$Chromosome==i)
+	if (length(tt)>0) {
+	  myMedianRatio=weirdNum
+	  mySegNUmber=0
+	  for (j in c(1:length(tt))) {
+	    if (ratio$MedianRatio[tt][j]!=myMedianRatio) {
+	      #print the record if it is not -1 or weirdNum
+	      if (myMedianRatio != -1 & myMedianRatio != weirdNum) {
+	        cat(i,"\t", ratio$Start[tt][j-mySegNumber], "\t", ratio$Start[tt][j]-1,"\t",mySegNumber,"\t",log(myMedianRatio,2),"\n")
+	      }
+	      #update
+	      mySegNumber=1
+	      myMedianRatio=ratio$MedianRatio[tt][j]
+	    }
+	    else {
+	      #update:
+	      mySegNumber = mySegNumber+1
+	    }
+	  }
+	  #print the last segment
+	  if (myMedianRatio != -1 & myMedianRatio != weirdNum) {
+	    cat(i,"\t", ratio$Start[tt][j-mySegNumber], "\t", ratio$Start[tt][j-1],"\t",mySegNumber,"\t",log(myMedianRatio,2),"\n")
+	  }
+	}	  
+}