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2
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1 library(Biobase)
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2 library(GEOquery)
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3 library(GEOmetadb)
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4 library(limma)
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5 library(jsonlite)
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6 library(affy)
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7 library(dplyr)
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8 library(affyPLM)
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9
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10 cargs<-commandArgs()
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11 cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
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12 nbargs=length(cargs)
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13
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14 dataFile=cargs[[nbargs-9]]
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15 normalization=cargs[[nbargs-8]]
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16 conditionsFile=cargs[[nbargs-7]]
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17 annotation=cargs[[nbargs-6]]
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18 result_export_eset=cargs[[nbargs-5]]
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19 result=cargs[[nbargs-4]]
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20 result.path=cargs[[nbargs-3]]
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21 result.template=cargs[[nbargs-2]]
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22
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23 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
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24
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25 data=as.matrix(read.table(file = dataFile))
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26 conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
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27 htmlfile=readChar(result.template, file.info(result.template)$size)
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28
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29 colnames(conditions)=c("source_name_ch1","description")
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30 phenodata<-new("AnnotatedDataFrame",data=conditions)
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31
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32 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
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33
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34 if (normalization == "quantile") {
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35 eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
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36 } else if (normalization == "log2") {
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37 exprs(eset) = log2(exprs(eset))
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38 }
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39
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40 boxplotnorm="boxplotnorm.png"
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41 png(boxplotnorm,width=800,height = 400)
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42 par(mar=c(7,5,1,1))
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43 boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
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44 dev.off()
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45 htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
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46 file.copy(boxplotnorm,result.path)
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47
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48 plotMAnorm="plotMAnorm.png"
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49 nblines=length(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0)
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50 png(plotMAnorm,width=800,height =300*nblines )
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51 par(mfrow=c(nblines,3))
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52 #for (i in 1:length(colnames(data))){
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53 MAplot(eset)
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54 #}
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55
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56 dev.off()
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57 htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
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58 file.copy(plotMAnorm,result.path)
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59 #write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
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60 #saveConditions=c(condition1Name,condition2Name)
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61 save(eset,file=result_export_eset)
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62 write(htmlfile,result)
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63
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64 #l=list()
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65 #for(i in 1:length(esets))
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66 #{
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67 # l[[paste("study",i,sep="")]]<-res[[i]]
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68 #}
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69 #l[["Meta"]]=res[[length(res)-1]]
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70 #showVenn(res,file.path(temp.files.path,"venn.png"))
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71 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
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72 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
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73 #writeLines(c("</body></html>"),file.conn)
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74 #close(file.conn) |
