Mercurial > repos > bornea > prohits_dotplot_generator
view Dotplot_Release/Normalization_sigpreys.R @ 23:fbc857f87f52 draft
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author | bornea |
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date | Mon, 18 Apr 2016 10:49:29 -0400 |
parents | bc752a05f16d |
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#!/usr/bin/env Rscript #this programs normalizes a saint input file based on the spectral counts of "signficant" preys # that is, preys with an FDR <= the secondary cutoff as supplied to the dotplot script args <- commandArgs(trailingOnly = TRUE) d = read.delim(args[1], header=T, as.is=T) d <- d[d$BFDR <= as.numeric(args[2]),] baitn = 1 curr_bait <- d$Bait[1] s <- vector() s[1] = 0 for(i in 1:length(d$Bait)){ if(curr_bait != d$Bait[i]){ baitn <- baitn + 1 curr_bait <- d$Bait[i] s[baitn] <- d$AvgSpec[i] } else{ s[baitn] <- s[baitn] + d$AvgSpec[i] } } med.s = median(s) s = s / med.s d_n <- d baitn = 1 curr_bait <- d_n$Bait[1] for(i in 1:length(d_n$Bait)){ if(curr_bait != d_n$Bait[i]){ baitn <- baitn + 1 curr_bait <- d_n$Bait[i] d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn] } else{ d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn] } } #print normalized data to file write.table(d_n, file = "norm_saint.txt", sep="\t", quote=F, row.names=F)