Mercurial > repos > bornea > dotplot_runner
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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| children |
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| -1:000000000000 | 0:dfa3436beb67 |
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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 |