Mercurial > repos > bornea > dotplot_runner
comparison Dotplot_Release/Step1_data_reformating.R @ 0:dfa3436beb67 draft
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| author | bornea |
|---|---|
| date | Fri, 29 Jan 2016 09:56:02 -0500 |
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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 d = read.delim(args[1], header=T, sep="\t", as.is=T) | |
| 6 | |
| 7 ### Select Prey interactions were at least one Bait > Probability Threshold | |
| 8 | |
| 9 preylist=unique(c(d$PreyGene[d$BFDR <= as.numeric(args[2])])) | |
| 10 pid = d$PreyGene %in% preylist | |
| 11 d = d[pid,] | |
| 12 | |
| 13 bb = unique(d$Bait) | |
| 14 pp = unique(d$PreyGene) | |
| 15 | |
| 16 nbait = length(bb) | |
| 17 nprey = length(pp) | |
| 18 | |
| 19 ### Reformat the SAINToutput data into a spreadsheet | |
| 20 mat = matrix(0, nprey, nbait) | |
| 21 | |
| 22 n = nrow(d) | |
| 23 mb = match(d$Bait, bb) | |
| 24 mp = match(d$PreyGene, pp) | |
| 25 | |
| 26 ### Using the AvgSpec for the spectral counts | |
| 27 for(i in 1:n) { | |
| 28 mat[mp[i],mb[i]] = d$AvgSpec[i] | |
| 29 } | |
| 30 | |
| 31 rownames(mat) = pp | |
| 32 colnames(mat) = bb | |
| 33 | |
| 34 outfile <- paste(c(args[3]), "matrix.txt", sep="_") | |
| 35 ### The following file is the outcome of running this step. | |
| 36 write.table(mat, outfile, sep="\t", quote=F) | |
| 37 | |
| 38 | |
| 39 | |
| 40 | |
| 41 |