--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Contra/scripts/cn_analysis.v4.R	Thu Sep 13 02:31:43 2012 -0400
@@ -0,0 +1,228 @@
+# ----------------------------------------------------------------------#
+# Copyright (c) 2011, Richard Lupat & Jason Li.
+#
+# > Source License <
+# This file is part of CONTRA.
+#
+#    CONTRA is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    CONTRA is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with CONTRA.  If not, see <http://www.gnu.org/licenses/>.
+#
+# 
+#-----------------------------------------------------------------------#
+# Last Updated : 30 Sept 2011 17:00PM
+
+
+# Parameters Parsing (from Command Line)
+options <- commandArgs(trailingOnly = T)
+bins = as.numeric(options[1])
+rd.cutoff = as.numeric(options[2])
+min.bases = as.numeric(options[3])
+outf = options[4]
+sample.name = options[5]
+plotoption = options[6]
+actual.bin = as.numeric(options[7])
+min_normal_rd_for_call = as.numeric(options[8])
+min_tumour_rd_for_call = as.numeric(options[9])
+min_avg_cov_for_call = as.numeric(options[10])
+
+if (sample.name == "No-SampleName")
+	sample.name = ""
+
+if (sample.name != "")
+	sample.name = paste(sample.name, ".", sep="")
+
+# Setup output name
+out.f = paste(outf, "/table/", sample.name, "CNATable.", rd.cutoff,"rd.", min.bases,"bases.", bins,"bins.txt", sep="")
+pdf.out.f = paste(outf, "/plot/", sample.name, "densityplot.", bins, "bins.pdf", sep="")
+
+# Open and read input files
+# cnAverageFile = paste("bin", bins, ".txt", sep="")
+cnAverageFile = paste(outf,"/buf/bin",bins,".txt",sep="")
+boundariesFile = paste(outf,"/buf/bin",bins,".boundaries.txt",sep="")
+print (cnAverageFile)
+cn.average = read.delim(cnAverageFile, as.is=F, header=F)
+cn.boundary= read.delim(boundariesFile,as.is=F, header=F)
+
+# Apply thresholds and data grouping
+cn.average.aboveTs = cn.average[cn.average$V3>min.bases,]
+cn.average.list = as.matrix(cn.average.aboveTs$V4)
+
+# Get the mean and sd for each bins 
+cn.average.mean = c()
+cn.average.sd = c()
+cn.average.log= c()
+
+# Density Plots for each bins
+if (plotoption == "True"){
+	pdf(pdf.out.f)
+}
+for (j in 1:actual.bin){
+	cn.average.nth 	= as.matrix(cn.average.aboveTs[cn.average.aboveTs$V15==j,]$V4)
+	cn.coverage.nth	= as.matrix(cn.average.aboveTs[cn.average.aboveTs$V15==j,]$V11)
+	boundary.end   	= cn.boundary[cn.boundary$V1==j,]$V2
+	boundary.start 	= cn.boundary[cn.boundary$V1==(j-1),]$V2
+	boundary.mid	= (boundary.end+boundary.start)/2
+	if (plotoption == "True") {
+		plot_title = paste("density: bin", bins, sep="")
+		#plot(density(cn.average.nth),xlim=c(-5,5), title=plot_title)
+		plot(density(cn.average.nth),xlim=c(-5,5))
+	}
+	cn.average.mean = c(cn.average.mean, mean(cn.average.nth))
+#	cn.average.sd 	= c(cn.average.sd, sd(cn.average.nth))
+	cn.average.sd 	= c(cn.average.sd, apply(cn.average.nth,2,sd))
+	#cn.average.log 	= c(cn.average.log, boundary.mid)
+	cn.average.log	= c(cn.average.log, log(mean(cn.coverage.nth),2))
+}
+if (plotoption == "True"){
+	dev.off()
+}
+
+# Put the data's details into matrices 
+ids 		= as.matrix(cn.average.aboveTs$V1)
+exons 		= as.matrix(cn.average.aboveTs$V6)
+exons.pos 	= as.matrix(cn.average.aboveTs$V5)
+gs 		= as.matrix(cn.average.aboveTs$V2)
+number.bases	= as.matrix(cn.average.aboveTs$V3)
+mean		= as.matrix(cn.average.aboveTs$V4)
+sd 		= as.matrix(cn.average.aboveTs$V7)
+tumour.rd 	= as.matrix(cn.average.aboveTs$V8)
+tumour.rd.ori	= as.matrix(cn.average.aboveTs$V10)
+normal.rd	= as.matrix(cn.average.aboveTs$V9)
+normal.rd.ori 	= as.matrix(cn.average.aboveTs$V11)
+median		= as.matrix(cn.average.aboveTs$V12)
+MinLogRatio 	= as.matrix(cn.average.aboveTs$V13)
+MaxLogRatio 	= as.matrix(cn.average.aboveTs$V14)
+Bin 		= as.matrix(cn.average.aboveTs$V15)
+Chr 		= as.matrix(cn.average.aboveTs$V16)
+OriStCoordinate = as.matrix(cn.average.aboveTs$V17)
+OriEndCoordinate= as.matrix(cn.average.aboveTs$V18)
+
+# Linear Fit
+logratios.mean	= mean
+logcov.mean	= log2((normal.rd + tumour.rd)/2)
+fit.mean	= lm(logratios.mean ~ logcov.mean)
+fit.x		= fit.mean$coefficient[1]
+fit.y		= fit.mean$coefficient[2]
+
+adjusted.lr	= rep(NA, length(logratios.mean))
+for (j in 1:length(logratios.mean)){
+	fitted.mean	= fit.x + fit.y * logcov.mean[j]
+	adjusted.lr[j]	= logratios.mean[j] - fitted.mean
+}
+
+fit.mean2	= lm(adjusted.lr ~ logcov.mean)
+fit.mean.a	= fit.mean2$coefficient[1]
+fit.mean.b	= fit.mean2$coefficient[2]
+
+fit.mean.fn <- function(x, fit.a, fit.b){
+	result = fit.a + fit.b * x
+	return (result)
+}
+
+# Adjust SD based on the new adjusted log ratios
+logratios.sd	= c()
+logcov.bins.mean= c()
+for (j in 1:actual.bin){
+	lr.bins.mean	= as.matrix(adjusted.lr[cn.average.aboveTs$V15==j])
+#	logratios.sd	= c(logratios.sd, sd(lr.bins.mean))
+	logratios.sd	= c(logratios.sd, apply(lr.bins.mean,2,sd))
+
+	cn.coverage.tumour.nth = as.matrix(cn.average.aboveTs[cn.average.aboveTs$V15==j,]$V8)
+	cn.coverage.normal.nth = as.matrix(cn.average.aboveTs[cn.average.aboveTs$V15==j,]$V9)
+	cn.coverage.nth	= (cn.coverage.tumour.nth + cn.coverage.normal.nth) /2
+	logcov.bins.mean= c(logcov.bins.mean, log2(mean(cn.coverage.nth)))
+
+}
+
+logratios.sd.ori = logratios.sd
+if (length(logratios.sd) > 2) {
+	logratios.sd 	= logratios.sd[-length(logratios.sd)]
+}
+
+logcov.bins.mean.ori = logcov.bins.mean
+if (length(logcov.bins.mean) > 2){
+	logcov.bins.mean= logcov.bins.mean[-length(logcov.bins.mean)]
+}
+
+fit.sd		= lm(log2(logratios.sd) ~ logcov.bins.mean)
+fit.sd.a	= fit.sd$coefficient[1]
+fit.sd.b	= fit.sd$coefficient[2]
+
+fit.sd.fn <- function(x, fit.a, fit.b){
+	result = 2 ^ (fit.mean.fn(x, fit.a, fit.b))
+	return (result)
+}
+	
+# Get the P Values, called the gain/loss
+# with average and sd from each bins
+pVal.list = c()
+gain.loss = c()
+
+for (i in 1:nrow(cn.average.list)){
+	#print (i)
+	#logratio = cn.average.list[i]
+	#logcov	 = log(normal.rd.ori[i],2)
+	logratio = adjusted.lr[i]
+	logcov	 = logcov.mean[i]
+	exon.bin = Bin[i]
+
+	if (length(logratios.sd) > 1){	
+		pVal <- pnorm(logratio, fit.mean.fn(logcov, fit.mean.a, fit.mean.b), fit.sd.fn(logcov, fit.sd.a, fit.sd.b))
+	} else {
+		pVal <- pnorm(logratio, 0, logratios.sd[exon.bin])
+	}
+
+	if (pVal > 0.5){
+		pVal = 1-pVal
+		gain.loss = c(gain.loss, "gain")
+	} else {
+		gain.loss = c(gain.loss, "loss")
+	}
+	pVal.list = c(pVal.list, pVal*2)
+}
+
+# Get the adjusted P Values
+adjusted.pVal.list = p.adjust(pVal.list, method="BH")
+
+# Write the output into a tab-delimited text files
+outdf=data.frame(Targeted.Region.ID=ids,Exon.Number=exons,Gene.Sym=gs,Chr, OriStCoordinate, OriEndCoordinate, Mean.of.LogRatio=cn.average.list, Adjusted.Mean.of.LogRatio=adjusted.lr, SD.of.LogRatio=sd, Median.of.LogRatio=median, number.bases, P.Value=pVal.list ,Adjusted.P.Value=adjusted.pVal.list , gain.loss, tumour.rd, normal.rd, tumour.rd.ori, normal.rd.ori, MinLogRatio, MaxLogRatio, BinNumber = Bin)
+
+#min_normal_rd_for_call=5
+#min_tumour_rd_for_call=0
+#min_avg_cov_for_call=20
+outdf$tumour.rd.ori = outdf$tumour.rd.ori-0.5
+outdf$normal.rd.ori = outdf$normal.rd.ori-0.5
+wh.to.excl = outdf$normal.rd.ori < min_normal_rd_for_call
+wh.to.excl = wh.to.excl | outdf$tumour.rd.ori < min_tumour_rd_for_call
+wh.to.excl = wh.to.excl | (outdf$tumour.rd.ori+outdf$normal.rd.ori)/2 < min_avg_cov_for_call
+outdf$P.Value[wh.to.excl]=NA
+outdf$Adjusted.P.Value[wh.to.excl]=NA
+
+
+write.table(outdf,out.f,sep="\t",quote=F,row.names=F,col.names=T)
+
+#Plotting SD
+#a.sd.fn  	= rep(fit.sd.a, length(logratios.sd.ori))
+#b.sd.fn    	= rep(fit.sd.b, length(logratios.sd.ori)) 
+#sd.after.fit 	= fit.sd.fn(logcov.bins.mean.ori, fit.sd.a, fit.sd.b)
+#sd.out.f 	= paste(outf, "/plot/", sample.name, "sd.data_fit.", bins, "bins.txt", sep="")
+#sd.outdf 	= data.frame(SD.Before.Fit = logratios.sd.ori, Log.Coverage = logcov.bins.mean.ori, SD.After.Fit = sd.after.fit, a.for.fitting=a.sd.fn, b.for.fitting=b.sd.fn)
+#write.table(sd.outdf, sd.out.f,sep="\t", quote=F, row.names=F, col.names=T)
+
+
+#End of the script
+print ("End of cn_analysis.R")
+print (i)
+
+
+