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