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8
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1 #!/usr/bin/env Rscript
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2 # setup R error handling to go to stderr
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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4
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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7
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8 library("optparse")
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9
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10 ##### Read options
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11 option_list=list(
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12 make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
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13 make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
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14 make_option("--normalization",type="character",default=NULL,help="log2 transformation"),
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15 make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"),
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16 make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
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17 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
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18 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
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19 make_option("--htmltemplate",type="character",default="NULL",help="html template)")
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20
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21
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22 );
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23
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24
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25 opt_parser = OptionParser(option_list=option_list);
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26 opt = parse_args(opt_parser);
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2
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27
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8
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28 if(is.null(opt$input)){
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29 print_help(opt_parser)
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30 stop("input required.", call.=FALSE)
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31 }
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32
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33 if(is.null(opt$conditions)){
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34 print_help(opt_parser)
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35 stop("conditions input required.", call.=FALSE)
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36 }
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37
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38
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39 #loading libraries
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40 suppressPackageStartupMessages(require(GEOquery))
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2
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41
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8
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42 suppressPackageStartupMessages(require(Biobase))
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43 suppressPackageStartupMessages(require(GEOquery))
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44 suppressPackageStartupMessages(require(GEOmetadb))
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45 suppressPackageStartupMessages(require(limma))
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46 suppressPackageStartupMessages(require(jsonlite))
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47 suppressPackageStartupMessages(require(affy))
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48 suppressPackageStartupMessages(require(dplyr))
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49 suppressPackageStartupMessages(require(affyPLM))
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50
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51 dataFile=opt$input
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52 normalization=opt$normalization
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53 conditionsFile=opt$conditions
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54 annotation=opt$annotations
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55 result_export_eset=opt$rdataoutput
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56 result=opt$htmloutput
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57 result.path=opt$htmloutputpath
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58 result.template=opt$htmltemplate
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2
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59
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60 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
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61
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8
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62 data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE))
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2
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63 conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
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64 htmlfile=readChar(result.template, file.info(result.template)$size)
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65
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66 colnames(conditions)=c("source_name_ch1","description")
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67 phenodata<-new("AnnotatedDataFrame",data=conditions)
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68
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69 head(data)
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70 conditions
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71
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2
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72 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
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73
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74 if (normalization == "quantile") {
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75 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2")
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2
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76 } else if (normalization == "log2") {
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77 exprs(eset) = log2(exprs(eset))
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78 }
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79
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80 boxplotnorm="boxplotnorm.png"
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81 png(boxplotnorm,width=800,height = 400)
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82 par(mar=c(7,5,1,1))
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83 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
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84 dev.off()
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85 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
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86 file.copy(boxplotnorm,result.path)
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87
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88 plotMAnorm="plotMAnorm.png"
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89 nblines=length(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0)
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90 png(plotMAnorm,width=800,height =300*nblines )
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91 par(mfrow=c(nblines,3))
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8
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92 ##for (i in 1:length(colnames(data))){
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2
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93 MAplot(eset)
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94 #}
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95
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96 dev.off()
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97 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
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98 file.copy(plotMAnorm,result.path)
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99 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
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100 #saveConditions=c(condition1Name,condition2Name)
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101 save(eset,file=result_export_eset)
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102 write(htmlfile,result)
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103
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104 #l=list()
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105 #for(i in 1:length(esets))
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106 #{
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107 # l[[paste("study",i,sep="")]]<-res[[i]]
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108 #}
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109 #l[["Meta"]]=res[[length(res)-1]]
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110 #showVenn(res,file.path(temp.files.path,"venn.png"))
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111 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
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112 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
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113 #writeLines(c("</body></html>"),file.conn)
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114 #close(file.conn) |
