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4
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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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2
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4
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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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2
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9
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4
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10 ##### Read options
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11 option_list=list(
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12 make_option("--id",type="character",default=NULL,help="GSE ID from GEO databse (required)"),
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13 make_option("--transformation",type="character",default=NULL,help="log2 transformation (required)"),
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14 make_option("--data",type="character",default=NULL,help="A table containing the expression data"),
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15 make_option("--rdata",type="character",default="NULL",help="rdata object containing eset object"),
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16 make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment")
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17
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18 );
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2
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19
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20 opt_parser = OptionParser(option_list=option_list);
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21 opt = parse_args(opt_parser);
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22
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23 if(is.null(opt$id)){
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24 print_help(opt_parser)
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25 stop("GEOdata id required.", call.=FALSE)
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26 }
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2
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27
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4
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28 #loading libraries
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29 suppressPackageStartupMessages(require(GEOquery))
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30
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31 GEOQueryID=opt$id
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32 GEOQueryData=opt$data
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33 GEOQueryRData=opt$rdata
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34 conditionFile=opt$conditions
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35 transformation=opt$transformation
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36
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37 data1=getGEO(GEOQueryID)
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2
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38 eset=data1[[1]]
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39
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40 #check if datas are in log2 space
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41 normalization<-function(data){
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42 ex <- exprs(data)
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43 qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
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44 LogC <- (qx[5] > 100) ||
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45 (qx[6]-qx[1] > 50 && qx[2] > 0) ||
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46 (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
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47 if (LogC) { ex[which(ex <= 0)] <- NaN
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48 return (log2(ex)) } else {
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49 return (ex)
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50 }
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51 }
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52
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53 if (transformation=="auto"){
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54 exprs(eset)=normalization(eset)
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55 } else if (transformation=="yes"){
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56 exprs(eset)=log2(exprs(eset))
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57 }
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58
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59 matrixData=exprs(eset)
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60 write.table(matrixData,col.names=NA,row.names=TRUE,sep="\t",file=GEOQueryData)
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61
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62 #Construcion of condition file
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63 #if there is data in "source_name_ch1" field, we keep this data as a condition
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64 #else we keep the "description" field data.
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65 if (length(unique(tolower(pData(data1[[1]])["source_name_ch1"][,1])))>1)
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66 {
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67 conditions=pData(data1[[1]])["source_name_ch1"]
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68 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
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69 } else
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70 {
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71 conditions=pData(data1[[1]])["description"]
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72 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
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73 }
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74
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75 conditions[,1]=tolower(conditions[,1])
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76 pData(eset)["source_name_ch1"]=conditions
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77
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78 write.table(cbind(conditions,description),quote = FALSE,col.names = FALSE, row.names=TRUE,file=conditionFile,sep="\t")
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79 save(eset,conditions,file=GEOQueryRData) |
