comparison Dotplot_Release/Normalization_sigpreys.R @ 0:dfa3436beb67 draft

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author bornea
date Fri, 29 Jan 2016 09:56:02 -0500
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1 #!/usr/bin/env Rscript
2
3 #this programs normalizes a saint input file based on the spectral counts of "signficant" preys
4 # that is, preys with an FDR <= the secondary cutoff as supplied to the dotplot script
5
6 args <- commandArgs(trailingOnly = TRUE)
7
8 d = read.delim(args[1], header=T, as.is=T)
9 d <- d[d$BFDR <= as.numeric(args[2]),]
10
11 baitn = 1
12 curr_bait <- d$Bait[1]
13 s <- vector()
14 s[1] = 0
15 for(i in 1:length(d$Bait)){
16 if(curr_bait != d$Bait[i]){
17 baitn <- baitn + 1
18 curr_bait <- d$Bait[i]
19 s[baitn] <- d$AvgSpec[i]
20 }
21 else{
22 s[baitn] <- s[baitn] + d$AvgSpec[i]
23 }
24 }
25
26 med.s = median(s)
27 s = s / med.s
28
29 d_n <- d
30 baitn = 1
31 curr_bait <- d_n$Bait[1]
32 for(i in 1:length(d_n$Bait)){
33 if(curr_bait != d_n$Bait[i]){
34 baitn <- baitn + 1
35 curr_bait <- d_n$Bait[i]
36 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn]
37 }
38 else{
39 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn]
40 }
41 }
42
43 #print normalized data to file
44
45 write.table(d_n, file = "norm_saint.txt", sep="\t", quote=F, row.names=F)
46