annotate peca.R @ 0:f50bb34c1a37 draft

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author caleb-easterly
date Wed, 21 Feb 2018 16:29:34 -0500
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children 784c107c5861
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f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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1 #!/usr/bin/env Rscript
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2
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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3 library(PECA)
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5 # Set up R error handling to go to stderr
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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6 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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8 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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9 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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11 main <- function() {
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12 args <- commandArgs(trailingOnly = TRUE)
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14 # read first argument, which is quant file (proteins in rows, samples in columns)
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15 quant_file <- read.delim(args[1],
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16 na.strings = c("0", "NA"),
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17 sep = '\t')
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18
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19 # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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20 group1_ind_file <- read.csv(args[2], header = FALSE)[1, ]
f50bb34c1a37 planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
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21 group2_ind_file <- read.csv(args[3], header = FALSE)[1, ]
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23 # read 4th argument, which is output file name
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24 out_file <- args[4]
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25
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26 # get vectors of column names
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27 df_names <- colnames(quant_file)
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28 group1_names <- df_names[group1_ind_file]
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29 group2_names <- df_names[group2_ind_file]
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31 # run PECA_df
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32 # id column is first column (hard-coded)
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33 results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1])
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34
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35 # put add protein names column
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36 results$prot <- row.names(results)
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37 results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]
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38
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39 # write to output
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40 write.table(results, file=out_file,
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41 quote=FALSE,
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42 sep ='\t',
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43 row.names = FALSE)
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44 }
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46 main()