Mercurial > repos > bornea > dotplot_runner
comparison Dotplot_Release/Step2_data_filtering.R @ 0:dfa3436beb67 draft
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| author | bornea |
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| 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, as.is=T) | |
| 6 | |
| 7 d2 = d | |
| 8 d2s = d | |
| 9 | |
| 10 ss_cutoff <- as.numeric(args[2]) | |
| 11 ### Here I'm only going to take the preys which appeared in at least 2 baits with >args[2] counts | |
| 12 id = apply(d, 1, function(x) sum(x>ss_cutoff) >= 2) | |
| 13 id2 = apply(d, 1, function(x) sum(x>ss_cutoff) < 2) | |
| 14 d2 = d2[id, ] | |
| 15 d2s = d2s[id2, 0] | |
| 16 max.d2 = max(as.numeric(as.matrix(d2))) | |
| 17 d2 = d2 / max.d2 * 10 | |
| 18 | |
| 19 d3 = data.frame(PROT = rownames(d2), d2) | |
| 20 | |
| 21 outfile <- paste(c(args[3]), "dat", sep=".") | |
| 22 | |
| 23 ### The following file is the outcome of running this step. | |
| 24 write.table(d3, outfile, sep="\t", quote=F, row.names=F) | |
| 25 ### This is the final input file for nested cluster algorithm | |
| 26 | |
| 27 write.table(d2s, "singletons.txt", quote=F) | |
| 28 |