Mercurial > repos > jbrayet > maketssdist

changeset 64:bfb77b85dcdf draft

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author jbrayet
date Thu, 13 Aug 2015 05:22:17 -0400
parents 6ba0d604ce44
children 526de88709a8
files makeTSSdist.R
diffstat 1 files changed, 0 insertions(+), 485 deletions(-) [+]
line wrap: on
line diff
--- a/makeTSSdist.R	Thu Aug 13 05:07:37 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,485 +0,0 @@
-#!/usr/bin/env Rscript
-
-#usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks] [1 for pdf]
-args <- commandArgs(TRUE)
-#print (args)
-myStep <- type.convert(args[2])
-maxValue <- type.convert(args[3])
-
-dataTable <-read.table(file=paste(args[4],".genes.ClosestPeakDist", sep=""), header=TRUE);
-chip.genes.ClosestPeakDist<-data.frame(dataTable)
-ifReg <- 0
-if (length(unique(chip.genes.ClosestPeakDist$Reg))>1) {
- ifReg <- 1
-}
-ifControl <- 0
-
-#options(bitmapType='cairo')
-
-ifPDF <- 0
-if (length(args)>=8) {
-	ifPDF=args[8]
-}
-if (length(args)==7 & args[7]==1) {
-	ifPDF=1
-}
-
-suppressMessages(library(Hmisc))
-suppressMessages(library(Cairo))
-
-if (length(args)>=7 & args[7]!=1 & args[7]!=0) {
-  dataTable <-read.table(file=paste(args[7],".genes.ClosestPeakDist", sep=""), header=TRUE);
-  control.genes.ClosestPeakDist<-data.frame(dataTable)
-  ifControl <- 1
-}
-if (ifReg & ifControl) {
-  if (ifPDF==1) {
-	pdf(file = args[5], width = 19, height = 8, pointsize = 20, bg = "white")
-  } else {
-  	png(file = args[5], type="cairo", width = 1440 , height = 680, units = "px", pointsize = 20, bg = "white", res = NA)
-	plot(1:10)
-  }
-  op <- par(mfrow = c(2,3))
-} else {
-  if (ifPDF==1) {
-	pdf(file = args[5], width = 10, height = 13, pointsize = 20, bg = "white")
-  } else {
-  	png(file = args[5], type="cairo", width = 680, height = 880, units = "px", pointsize = 20, bg = "white", res = NA)
-	plot(1:10)
-  }
- # plot(1:10)
-  op <- par(mfrow = c(2,1))
-}
-myColor <- 1
-myColor[1] <- colors()[131]
-myColor[2] <- "darkolivegreen3"
-myColor[3] <- "azure4"
-myColor[4] <- "royalblue3"
-myColor[5] <- colors()[17]
-
-myColorControl <- 1
-
-myColorControl[1] <- colors()[24]
-myColorControl[2] <- colors()[278]
-myColorControl[3] <- colors()[305]
-myColorControl[4] <- colors()[219]
-myColorControl[5] <- colors()[343]
-
-
-
-#for cumulative:
-dist_real_f <- chip.genes.ClosestPeakDist
-if (ifControl) {
- dist_control_f <- control.genes.ClosestPeakDist
-}
-step <- myStep
-lim <- maxValue
-x <- 0
-count <- 1
-countL <-1
-n.types <- 1
-myLevels <- 0
-countTotalCont <- 0
-countTotal <-0
-countLCont <- 0
-cumTotalCont <- 0
-if (ifReg) {
-	 n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
-	 myLevels <- levels(chip.genes.ClosestPeakDist$Reg)
-	 cum = matrix( 0, nrow=lim/step +1,  ncol=n.types, byrow = TRUE) 
-	 for (i in c(1:n.types)) {
-	 	t <- which ((dist_real_f$Reg==myLevels[i]))
-	 	countL[i] <- length(t)
-         }	
-	count <-1 
-	for (i in seq(length=lim/step +1, from=0, by=step)) {
-		for (t in c(1:n.types)) {
-			tt <- which ((dist_real_f$Reg==myLevels[t])&(dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
-			cum[count,t] <- length(tt)	 		
-         	}		
-		x[count] <- i
-		count <- count + 1
-	}
-	ymax <- max(cum[,1]/countL[1], na.rm=TRUE)
-	for (i in c(2:n.types)) {
-	 	ymax <- max(ymax,max(cum[,i]/countL[i], na.rm=TRUE))
-         }
-	myLocCol <- myColor[2]	
-
-	par(mar=c(5.1, 7.1, 4.1, 2.1)) 
-
-	 plot (x,cum[,1]/countL[1] ,col = myColor[2],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" , ylim=c(0,ymax))
-	 for (i in c(2:n.types)) {
-	 	colorr <- i+1
-		myLocCol <- c(myLocCol,myColor[colorr])
-		lines (x,cum[,i]/countL[i] ,col = myColor[colorr],type="l", lwd = 2)
-#		print (myColor[colorr])
-         }	
-	
-	gradi <- 1000
-	if (lim>10000) {
-		gradi <- 10000
-	}
-	if (lim<3000) {
-		gradi <- 500
-	}
-	 axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
-  	 axisxlab <- paste(axisx/1000,"", sep = "")
-   	 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-  	 ymax <- max(cum[,i]/countL[i], na.rm=TRUE)
-
-	  minor.tick(nx=5,tick.ratio=0.5)
-
-	 legend(lim*0.45, ymax*0.45, myLevels,  cex=1, lwd = 2, bty = "n", col = myLocCol, lty = c(1),  pt.bg= c(myLocCol) , merge = TRUE)
-
-	title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
-	
-	 if (ifControl) {
-                count <-1
- 	 	n.types <- length(levels(control.genes.ClosestPeakDist$Reg))
-	 	myLevels <- levels(control.genes.ClosestPeakDist$Reg)
-		 cumCont = matrix( 0, nrow=lim/step +1,  ncol=n.types, byrow = TRUE) 
-		 for (i in c(1:n.types)) {
-		 	t <- which ((dist_control_f$Reg==myLevels[i]))
-		 	countLCont[i] <- length(t)
-		 }	 
-		for (i in seq(length=lim/step +1, from=0, by=step)) {
-			for (t in c(1:n.types)) {
-				tt <- which ((dist_control_f$Reg==myLevels[t])&(dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
-				cumCont[count,t] <- length(tt)	 		
-		 	}		
-			x[count] <- i
-			count <- count + 1
-		}
-		ymax <- max(cumCont[,1]/countLCont[1], na.rm=TRUE)
-		for (i in c(2:n.types)) {
-		 	ymax <- max(ymax,max(cumCont[,i]/countLCont[i], na.rm=TRUE))
-		 }
-		myLocColCntr <- myColorControl[2]	
-		plot (x,cumCont[,1]/countLCont[1] ,col = myLocColCntr[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" , ylim=c(0,ymax))
-		 for (i in c(2:n.types)) {
-		 	colorr <- i+1
-			myLocColCntr <- c(myLocColCntr,myColorControl[colorr])
-			lines (x,cumCont[,i]/countLCont[i] ,col = myColorControl[colorr],type="l", lwd = 2)
-		 }	
-	   	   if (lim>10000) {
-				gradi <- 10000
-		   }
-		   if (lim<3000) {
-				gradi <- 500
-		   }
-		   axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
-	  	 axisxlab <- paste(axisx/1000, sep = "")
-	   	 axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-  		minor.tick(nx=5,tick.ratio=0.5)
-		legend(lim*0.45, ymax*0.45, myLevels,  cex=1 , lwd = 2, bty = "n", col = myLocColCntr, lty = c(1),  pt.bg= c(myLocCol) , merge = TRUE)
-		title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
-		#real_vs_control_cumulative:
-		count <-1
-		countTotal <- length(dist_real_f$Reg)
-	   	cumTotal  <- 0
-		for (i in seq(length=lim/step +1, from=0, by=step)) {	
-			t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
-			cumTotal[count] <- length(t)
-			x[count] <- i
-			count <- count + 1
-		}
-		   plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
-		   gradi <- 1000
-		   if (lim>10000) {
-				gradi <- 10000
-		    }
-		    if (lim<3000) {
-				gradi <- 500
-		    }
-		    axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
-		   axisxlab <- paste(axisx/1000, sep = "")
-		   axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-		   ymax <- max(cumTotal/countTotal, na.rm=TRUE)
-    		 minor.tick(nx=5,tick.ratio=0.5)
-		countTotalCont <- length(dist_control_f$Reg)
-	   	cumTotalCont  <- 0
-		count <- 1
-		for (i in seq(length=lim/step +1, from=0, by=step)) {	
-			t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
-			cumTotalCont[count] <- length(t)
-			x[count] <- i
-			count <- count + 1
-		}
-		lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
-		legend(lim*0.45, ymax*0.45, c("ChIP","Control"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1),  pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
-		title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
-	}
-} else {
-   countTotal <- length(dist_real_f$Reg)
-   cumTotal  <- 0
-   count <-1
-
-   gradi <- 1000
-   if (lim>10000) {
-	gradi <- 10000
-   }
-   if (lim<3000) {
-	gradi <- 500
-   }
-
-   for (i in seq(length=lim/step +1, from=0, by=step)) {	
-	t <- which ((dist_real_f$Dist<=i)&(dist_real_f$Dist>=-i))
-	cumTotal[count] <- length(t)
-	x[count] <- i
-	count <- count + 1
-   }
-   par(mar=c(5.1, 7.1, 4.1, 2.1)) 
-  
-   plot (x,cumTotal/countTotal ,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(0, lim),xaxt="n" )
-   axisx <- seq(length=lim/gradi+1, from=0, by=gradi)
-   axisxlab <- paste(axisx/1000, sep = "")
-   axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (cumulative)")
-   ymax <- max(cumTotal/countTotal, na.rm=TRUE)
-   if (ifControl) {
-	countTotalCont <- length(dist_control_f$Reg)
-   	cumTotalCont  <- 0
-	count <- 1
-	for (i in seq(length=lim/step +1, from=0, by=step)) {	
-		t <- which ((dist_control_f$Dist<=i)&(dist_control_f$Dist>=-i))
-		cumTotalCont[count] <- length(t)
-		x[count] <- i
-		count <- count + 1
-	}
-	lines (x,cumTotalCont/countTotalCont ,col = colors()[328],type="l", lwd = 2)
-        legend(lim*0.45, ymax*0.45, c("ChIP","Control"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1),  pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
-   } else {
-        legend(lim*0.45, ymax*0.45, c("ChIP"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1]), lty = c(1),  pt.bg= c(myColor[1]) , merge = TRUE)
-   }
-}
-
-sink(args[6], append=FALSE, split=FALSE)
-if (ifReg) {
-	if (ifControl) {
-		cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
-		cat("\t")
- 		for (i in c(1:n.types)) {
-		 	cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", sep=""))
-                	cat("\t")
-		}	
-
- 		for (i in c(1:n.types)) {
-		 	cat(paste("% ", myLevels[i]," genes w/ a peak in Control", sep=""))
-			cat("\t")
-		}
-                cat("\n")
-		for (i in c(1:length(x))) {
-			cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
-                	cat("\t")
-	 		for (t in c(1:n.types)) {
-			 	cat(paste(cum[i,t]/countL[t],"\t", sep=""))
-			}
-	 		for (t in c(1:n.types)) {
-			 	cat(paste(cumCont[i,t]/countLCont[t],"\t", sep=""))
-			}	 		
-                	cat("\n")
-		}
-	}else {
-            cat (paste("Dist_TSS","\t",sep=''))
- 	    for (i in c(1:n.types)) {
-		 cat(paste("% ", myLevels[i]," genes w/ a peak in ChIP", "\t", sep=""))
-	    }
- 	    cat("\n")
-	    for (i in c(1:length(x))) {
-			cat(paste(x[i],"\t",sep=""))	 		
-	 		for (t in c(1:n.types)) {
-			 	cat(paste(cum[i,t]/countL[t],"\t", sep=""))
-			}
-                	cat("\n")
-	    }
-	}
-} else {
-	if (ifControl) {
-		cat (paste("Dist_TSS","% genes w/ a peak in ChIP","% genes w/ a peak in control",sep='\t'))
-                cat("\n")
-		for (i in c(1:length(x))) {
-			cat(paste(x[i],cumTotal[i]/countTotal,cumTotalCont[i]/countTotalCont,sep="\t"))
-                	cat("\n")
-		}
-	}else {
-		cat (paste("Dist_TSS","% genes w/ a peak in ChIP",sep='\t'))
-                cat("\n")
-		for (i in c(1:length(x))) {
-			cat(paste(x[i],cumTotal[i]/countTotal,sep="\t"))
-                	cat("\n")
-		}
-
-	}
-}
-
-
-#stop sinking:
-sink() 
-
-#around TSS:
-lim <- maxValue
-step <- myStep
-my_breaks <- seq(length=lim/step*2 +1, from=-lim, by=step)
-chip.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;
-dist_real_f <- chip.genes
-if (ifControl) {
-   control.genes <- read.table(file=paste(args[4],".genes", sep=""), header=TRUE) ;   
-   dist_control_f<-data.frame(control.genes)
-}
-if (ifReg) {
-	#n.types <- length(levels(chip.genes.ClosestPeakDist$Reg))
-	 #myLevels <- levels(dist_real_f$Reg)
-
-	t<- which (dist_real_f$Reg==myLevels[1])
-	values_real <-dist_real_f$Dist[t]
-	hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real))  )
-        ymax <- max(hTSSreal$density, na.rm=TRUE)
-	for (i in c(2:n.types)) {
-		t<- which (dist_real_f$Reg==myLevels[i])
-		values_real <-dist_real_f$Dist[t]
-		hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real))  )
-        	ymax <- max(ymax,max(hTSSreal$density, na.rm=TRUE))
-        }
-
-
-	t<- which (dist_real_f$Reg==myLevels[1])
-	values_real <-dist_real_f$Dist[t]
-	hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real))  ) 
-        plot (hTSSreal$mids,hTSSreal$density,col = myLocCol[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),ylim = c(0, ymax), xaxt="n" ) 
-	
-	title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")
-
-	for (i in c(2:n.types)) {
-		t<- which (dist_real_f$Reg==myLevels[i])
-		values_real <-dist_real_f$Dist[t]
-		hTSSreal = hist(values_real,plot=FALSE,breaks = c(min(values_real),my_breaks,max(values_real))  )
-  		lines (hTSSreal$mids,hTSSreal$density,col = myLocCol[i],type="l", lwd = 2)
-        }
-	legend(lim*0.1, ymax*0.9, myLevels,  cex=1 , lwd = 2, bty = "n", col = myLocCol, lty = c(1),  pt.bg= c(myLocCol) , merge = TRUE)
-		
-	   gradi <- 1000
-	   if (lim>10000) {
-		gradi <- 10000
-	   }
-	   if (lim<3000) {
-		gradi <- 500
-	   }
-
-	   axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
-      	   axisxlab <- paste(axisx/1000, sep = "")
-	   axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-
-
-  	#minor.tick(nx=10,tick.ratio=0.5)
-       if (ifControl) {
-		t<- which (dist_control_f$Reg==myLevels[1])
-		values_control <-dist_control_f$Dist[t]
-		hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control))  )
-		ymax <- max(hTSScontrol$density, na.rm=TRUE)
-		for (i in c(2:n.types)) {
-			t<- which (dist_control_f$Reg==myLevels[i])
-			values_control <-dist_control_f$Dist[t]
-			hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control))  )
-			ymax <- max(ymax,max(hTSScontrol$density, na.rm=TRUE))
-		}
-		t<- which (dist_control_f$Reg==myLevels[1])
-		values_control <-dist_control_f$Dist[t]
-		hTSScontrol= hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control))  )
-		plot (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),ylim = c(0, ymax),xaxt="n" ) 
-		title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")		
-		for (i in c(2:n.types)) {
-			t<- which (dist_control_f$Reg==myLevels[i])
-			values_control <-dist_control_f$Dist[t]
-			hTSScontrol = hist(values_control,plot=FALSE,breaks = c(min(values_control),my_breaks,max(values_control))  )
-	  		lines (hTSScontrol$mids,hTSScontrol$density,col = myLocColCntr[i],type="l", lwd = 2)
-		}
-
-		gradi <- 1000
-		   if (lim>10000) {
-			gradi <- 10000
-		   }
-		   if (lim<3000) {
-			gradi <- 500
-		   }
-
-		   axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
-	      	   axisxlab <- paste(axisx/1000, sep = "")
-		   axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-
-		legend(lim*0.1, ymax*0.9, myLevels,  cex=1 , lwd = 2, bty = "n", col = myLocColCntr, lty = c(1),  pt.bg= c(myLocCol) , merge = TRUE)
-		
-	  	# minor.tick(nx=10,tick.ratio=0.5)
-		#control vs real
-		 values_real <-dist_real_f$Dist
-		 hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real))  )
-		 plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n") 
-		title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")		
-		 ymax <- max(hTSSreal$density, na.rm=TRUE)
-		  values_control <-dist_control_f$Dist
-		  hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control))  )
-		  lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
-		  legend(lim*0.2, ymax*0.9, c("ChIP","Control"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1),  pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)		 
-		
-		   gradi <- 1000
-		   if (lim>10000) {
-			gradi <- 10000
-		   }
-		   if (lim<3000) {
-			gradi <- 500
-		   }
-
-		   axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
-	      	   axisxlab <- paste(axisx/1000, sep = "")
-		   axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-
-
-
-		 # minor.tick(nx=10,tick.ratio=0.5)
-       }
-} else {
- values_real <-dist_real_f$Dist
- hTSSreal = hist(values_real, plot=FALSE, breaks = c(min(values_real),my_breaks,max(values_real))  )
- plot (hTSSreal$mids,hTSSreal$density,col = myColor[1],type="l", main="",xlab="",ylab="", lwd = 2, xlim = c(-lim, lim),xaxt="n") 
-		title( main="",xlab="Distance from TSS (Kb)",ylab="Proportion of genes with a peak\nat a given distance (density)")		
- ymax <- max(hTSSreal$density, na.rm=TRUE)
- if (ifControl) {
-  values_control <-dist_control_f$Dist
-  hTSScontrol = hist(values_control, plot=FALSE, breaks = c(min(values_control),my_breaks,max(values_control))  )
-  lines (hTSScontrol$mids,hTSScontrol$density,col = colors()[328],type="l", lwd = 2)
-  legend(lim*0.2, ymax*0.9, c("ChIP","Control"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1], colors()[328]), lty = c(1),  pt.bg= c(myColor[1], colors()[328]) , merge = TRUE)
- } else {
-  legend(lim*0.2, ymax*0.9, c("ChIP"),  cex=1 , lwd = 2, bty = "n", col = c(myColor[1]), lty = c(1),  pt.bg= c(myColor[1]) , merge = TRUE)
- }
-
- gradi <- 1000
- if (lim>10000) {
-    gradi <- 10000
-  }
-  if (lim<3000) {
-	gradi <- 500
-  }
-
-  axisx <- seq(length=2*lim/gradi+1, from=-lim, by=gradi)
-  axisxlab <- paste(axisx/1000, sep = "")
-  axis(1, at=axisx,labels=axisxlab , las=1, cex.axis=1)
-
-
- # minor.tick(nx=10,tick.ratio=0.5)
-}
-suppressMessages(dev.off())
-q();
-cat (paste("peak height","# peaks in ChIP","# peaks in Control","#control/chip","\n",sep='\t'))
-for (xval in c(minValue:maxValue)) {
-  for (i in (1:length(chipHist$mids))) {     
-     if (xval==chipHist$mids[i]) {
-      ychip <- chipHist$counts[i]
-     }
-  }
-  for (i in (1:length(controlHist$mids))) {     
-     if (xval==controlHist$mids[i]) {
-      ycontrol <- controlHist$counts[i]
-     }
-  }
-  cat (paste(xval,ychip,ycontrol,ycontrol/ychip,"\n",sep='\t'))
-}