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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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5
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6 library('getopt');
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7 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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8 args <- commandArgs(trailingOnly = TRUE)
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9
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10 #get options, using the spec as defined by the enclosed list.
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11 #we read the options from the default: commandArgs(TRUE).
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12 spec = matrix(c(
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13 'verbose', 'v', 2, "integer",
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14 'help' , 'h', 0, "logical",
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15 'outfile' , 'o', 1, "character",
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16 'plots' , 'p', 2, "character",
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17 'infile' , 'i', 1, "character",
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18 'format', 'f', 1, 'character'
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19 ), byrow=TRUE, ncol=4);
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20
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21 opt = getopt(spec);
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22
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23 # if help was asked for print a friendly message
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24 # and exit with a non-zero error code
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25 if ( !is.null(opt$help) ) {
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26 cat(getopt(spec, usage=TRUE));
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27 q(status=1);
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28 }
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29
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30
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31 library('DiffBind')
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32 # used to save to BED, GFF or WIG format
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33
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34 if ( !is.null(opt$plots) ) {
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35 pdf(opt$plots)
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36 }
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37
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38
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39 sample = dba(sampleSheet=opt$infile, peakFormat='bed')
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40 sample_count = dba.count(sample)
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41 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
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42 sample_analyze = dba.analyze(sample_contrast)
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43 diff_bind = dba.report(sample_analyze)
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44 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE)
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45
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46 resSorted <- diff_bind[order(diff_bind$FDR),]
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47 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE)
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48
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49
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50 dev.off()
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51 sessionInfo()
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