|
2
|
1
|
|
|
2 library(GEOquery)
|
|
|
3
|
|
|
4
|
|
|
5 cargs<-commandArgs()
|
|
|
6 cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
|
|
|
7
|
|
|
8 GEOQueryID<-cargs[[1]]
|
|
|
9 GEOQueryData<-cargs[[2]]
|
|
|
10 GEOQueryRData<-cargs[[3]]
|
|
|
11 conditionFile<-cargs[[4]]
|
|
|
12 transformation<-cargs[[5]]
|
|
|
13
|
|
|
14 data1 = getGEO(GEOQueryID)
|
|
|
15 eset=data1[[1]]
|
|
|
16
|
|
|
17 #check if datas are in log2 space
|
|
|
18 normalization<-function(data){
|
|
|
19 ex <- exprs(data)
|
|
|
20 qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
|
|
|
21 LogC <- (qx[5] > 100) ||
|
|
|
22 (qx[6]-qx[1] > 50 && qx[2] > 0) ||
|
|
|
23 (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
|
|
|
24 if (LogC) { ex[which(ex <= 0)] <- NaN
|
|
|
25 return (log2(ex)) } else {
|
|
|
26 return (ex)
|
|
|
27 }
|
|
|
28 }
|
|
|
29
|
|
|
30 if (transformation=="auto"){
|
|
|
31 exprs(eset)=normalization(eset)
|
|
|
32 } else if (transformation=="yes"){
|
|
|
33 exprs(eset)=log2(exprs(eset))
|
|
|
34 }
|
|
|
35
|
|
|
36 matrixData=exprs(eset)
|
|
|
37 write.table(matrixData,col.names=NA,row.names=TRUE,sep="\t",file=GEOQueryData)
|
|
|
38
|
|
|
39 #Construcion of condition file
|
|
|
40 #if there is data in "source_name_ch1" field, we keep this data as a condition
|
|
|
41 #else we keep the "description" field data.
|
|
|
42 if (length(unique(tolower(pData(data1[[1]])["source_name_ch1"][,1])))>1)
|
|
|
43 {
|
|
|
44 conditions=pData(data1[[1]])["source_name_ch1"]
|
|
|
45 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
|
|
|
46 } else
|
|
|
47 {
|
|
|
48 conditions=pData(data1[[1]])["description"]
|
|
|
49 description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
|
|
|
50 }
|
|
|
51
|
|
|
52 conditions[,1]=tolower(conditions[,1])
|
|
|
53 pData(eset)["source_name_ch1"]=conditions
|
|
|
54
|
|
|
55 write.table(cbind(conditions,description),quote = FALSE,col.names = FALSE, row.names=TRUE,file=conditionFile,sep="\t")
|
|
|
56 save(eset,conditions,file=GEOQueryRData) |
