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1 #!/usr/bin/env Rscript
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2
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3 args <- commandArgs(trailingOnly = TRUE)
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4
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5 d = read.delim(args[1], header=T, sep="\t", as.is=T)
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6
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7 ### Select Prey interactions were at least one Bait > Probability Threshold
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8
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9 preylist=unique(c(d$PreyGene[d$BFDR <= as.numeric(args[2])]))
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10 pid = d$PreyGene %in% preylist
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11 d = d[pid,]
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12
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13 bb = unique(d$Bait)
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14 pp = unique(d$PreyGene)
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15
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16 nbait = length(bb)
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17 nprey = length(pp)
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18
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19 ### Reformat the SAINToutput data into a spreadsheet
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20 mat = matrix(0, nprey, nbait)
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21
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22 n = nrow(d)
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23 mb = match(d$Bait, bb)
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24 mp = match(d$PreyGene, pp)
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25
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26 ### Using the AvgSpec for the spectral counts
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27 for(i in 1:n) {
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28 mat[mp[i],mb[i]] = d$AvgSpec[i]
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29 }
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30
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31 rownames(mat) = pp
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32 colnames(mat) = bb
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33
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34 outfile <- paste(c(args[3]), "matrix.txt", sep="_")
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35 ### The following file is the outcome of running this step.
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36 write.table(mat, outfile, sep="\t", quote=F)
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37
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38
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40
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