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annotate diffbind.R @ 20:11cd8b1ae397 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
author iuc
date Sun, 28 Jan 2018 04:25:49 -0500
parents a8dc71379df0
children
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1 ## Setup R error handling to go to stderr
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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6 suppressPackageStartupMessages({
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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7 library('getopt')
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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8 library('DiffBind')
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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9 })
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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12 args <- commandArgs(trailingOnly = TRUE)
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14 #get options, using the spec as defined by the enclosed list.
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15 #we read the options from the default: commandArgs(TRUE).
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16 spec = matrix(c(
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17 'verbose', 'v', 2, "integer",
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18 'help' , 'h', 0, "logical",
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19 'outfile' , 'o', 1, "character",
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20 'plots' , 'p', 2, "character",
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21 'infile' , 'i', 1, "character",
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11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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22 'format', 'f', 1, "character",
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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23 'th', 't', 1, "double",
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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24 'bmatrix', 'b', 0, "logical"
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25 ), byrow=TRUE, ncol=4);
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27 opt = getopt(spec);
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28
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29 # if help was asked for print a friendly message
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30 # and exit with a non-zero error code
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31 if ( !is.null(opt$help) ) {
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32 cat(getopt(spec, usage=TRUE));
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33 q(status=1);
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34 }
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36 if ( !is.null(opt$plots) ) {
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37 pdf(opt$plots)
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38 }
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40 sample = dba(sampleSheet=opt$infile, peakFormat='bed')
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41 sample_count = dba.count(sample)
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42 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
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43 sample_analyze = dba.analyze(sample_contrast)
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44 diff_bind = dba.report(sample_analyze)
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45 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
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47 resSorted <- diff_bind[order(diff_bind$FDR),]
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48 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)
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11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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50 # Output binding affinity scores
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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51 if (!is.null(opt$bmatrix)) {
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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52 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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53 write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 11
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54 }
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56 dev.off()
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57 sessionInfo()