Mercurial > repos > bornea > dotplot_runner
comparison Dotplot_Release/Normalization.R @ 0:dfa3436beb67 draft
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| author | bornea |
|---|---|
| date | Fri, 29 Jan 2016 09:56:02 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:dfa3436beb67 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 args <- commandArgs(trailingOnly = TRUE) | |
| 4 | |
| 5 #this programs normalizes a saint input file based on the spectral counts of all preys | |
| 6 | |
| 7 d = read.delim(args[1], header=T, sep="\t", as.is=T) | |
| 8 | |
| 9 baitn = 1 | |
| 10 curr_bait <- d$Bait[1] | |
| 11 s <- vector() | |
| 12 s[1] = 0 | |
| 13 for(i in 1:length(d$Bait)){ | |
| 14 if(curr_bait != d$Bait[i]){ | |
| 15 baitn <- baitn + 1 | |
| 16 curr_bait <- d$Bait[i] | |
| 17 s[baitn] <- d$AvgSpec[i] | |
| 18 } | |
| 19 else{ | |
| 20 s[baitn] <- s[baitn] + d$AvgSpec[i] | |
| 21 } | |
| 22 } | |
| 23 | |
| 24 med.s = median(s) | |
| 25 s = s / med.s | |
| 26 | |
| 27 d_n <- d | |
| 28 baitn = 1 | |
| 29 curr_bait <- d_n$Bait[1] | |
| 30 for(i in 1:length(d_n$Bait)){ | |
| 31 if(curr_bait != d_n$Bait[i]){ | |
| 32 baitn <- baitn + 1 | |
| 33 curr_bait <- d_n$Bait[i] | |
| 34 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn] | |
| 35 } | |
| 36 else{ | |
| 37 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn] | |
| 38 } | |
| 39 } | |
| 40 | |
| 41 #print normalized data to file | |
| 42 | |
| 43 write.table(d_n, file = "norm_saint.txt", sep="\t", quote=F, row.names=F) | |
| 44 |