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annotate Recount.R @ 34:0a74b8de4c10 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
author sblanck
date Thu, 21 Jun 2018 10:41:50 -0400
parents 2d7595c8041d
children
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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1 #!/usr/bin/env Rscript
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2 # setup R error handling to go to stderr
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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8 library("optparse")
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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10 ##### Read options
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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11 option_list=list(
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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12 make_option("--id",type="character",default=NULL,help="GSE ID from GEO databse (required)"),
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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13 make_option("--report",type="character",default=NULL,help="Text file summarizing conditions of the experiment")
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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15 );
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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17 opt_parser = OptionParser(option_list=option_list);
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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18 opt = parse_args(opt_parser);
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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20 if(is.null(opt$id)){
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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21 print_help(opt_parser)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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22 stop("Recount id required.", call.=FALSE)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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23 }
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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25 #loading libraries
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0a74b8de4c10 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
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26 suppressPackageStartupMessages(require(recount))
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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28 studyID=opt$id
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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29 reportFile=opt$report
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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31 dir.create("./split", showWarnings = TRUE, recursive = FALSE)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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33 url <- download_study(studyID)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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34 load(file.path(studyID, 'rse_gene.Rdata'))
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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35 rse <- scale_counts(rse_gene)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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36 counts=assay(rse)
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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37 conditions=rse$title
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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39 for (i in 1:ncol(counts))
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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40 {
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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41 currentCount=as.data.frame(counts[,i])
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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42 sampleID=colnames(counts)[i]
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0a74b8de4c10 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
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43 #colnames(currentCount)=sampleID
0a74b8de4c10 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
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44 write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i],'.tabular'),sep="\t",row.names = T, col.names = F)
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45 }
2d7595c8041d planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71
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46
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0a74b8de4c10 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
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47 write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t")