--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dotplot_Release/Step1_data_reformating.R	Fri Jan 29 09:56:02 2016 -0500
@@ -0,0 +1,41 @@
+#!/usr/bin/env Rscript
+
+args <- commandArgs(trailingOnly = TRUE)
+
+d = read.delim(args[1], header=T, sep="\t", as.is=T)
+
+### Select Prey interactions were at least one Bait > Probability Threshold
+
+preylist=unique(c(d$PreyGene[d$BFDR <= as.numeric(args[2])]))
+pid = d$PreyGene %in% preylist
+d = d[pid,]
+
+bb = unique(d$Bait)
+pp = unique(d$PreyGene)
+
+nbait = length(bb)
+nprey = length(pp)
+
+### Reformat the SAINToutput data into a spreadsheet
+mat = matrix(0, nprey, nbait)
+
+n = nrow(d)
+mb = match(d$Bait, bb)
+mp = match(d$PreyGene, pp)
+
+### Using the AvgSpec for the spectral counts
+for(i in 1:n) {
+	mat[mp[i],mb[i]] = d$AvgSpec[i]	
+}
+
+rownames(mat) = pp
+colnames(mat) = bb
+
+outfile <- paste(c(args[3]), "matrix.txt", sep="_")
+### The following file is the outcome of running this step.
+write.table(mat, outfile, sep="\t", quote=F)
+
+
+
+
+