diff GEOQuery.R @ 2:93451f832736 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOQuery.R	Tue Mar 21 10:28:47 2017 -0400
@@ -0,0 +1,56 @@
+
+library(GEOquery)
+
+
+cargs<-commandArgs()
+cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
+
+GEOQueryID<-cargs[[1]]
+GEOQueryData<-cargs[[2]]
+GEOQueryRData<-cargs[[3]]
+conditionFile<-cargs[[4]]
+transformation<-cargs[[5]]
+
+data1 = getGEO(GEOQueryID)
+eset=data1[[1]]
+
+#check if datas are in log2 space
+normalization<-function(data){
+	ex <- exprs(data)
+	qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
+	LogC <- (qx[5] > 100) ||
+			(qx[6]-qx[1] > 50 && qx[2] > 0) ||
+			(qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
+	if (LogC) { ex[which(ex <= 0)] <- NaN
+		return (log2(ex)) } else {
+		return (ex)
+	}
+}
+
+if (transformation=="auto"){
+	exprs(eset)=normalization(eset)
+} else if (transformation=="yes"){
+	exprs(eset)=log2(exprs(eset))			
+}
+
+matrixData=exprs(eset)
+write.table(matrixData,col.names=NA,row.names=TRUE,sep="\t",file=GEOQueryData)
+
+#Construcion of condition file
+#if there is data in "source_name_ch1" field, we keep this data as a condition
+#else we keep the "description" field data.
+if (length(unique(tolower(pData(data1[[1]])["source_name_ch1"][,1])))>1)
+{
+	conditions=pData(data1[[1]])["source_name_ch1"]
+	description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
+}	else
+{
+	conditions=pData(data1[[1]])["description"]
+	description=paste0(as.vector(pData(data1[[1]])["geo_accession"][,1]), " ",as.vector(pData(data1[[1]])["title"][,1]), " ", as.vector(conditions[,1]))
+}
+
+conditions[,1]=tolower(conditions[,1])
+pData(eset)["source_name_ch1"]=conditions
+
+write.table(cbind(conditions,description),quote = FALSE,col.names = FALSE, row.names=TRUE,file=conditionFile,sep="\t")
+save(eset,conditions,file=GEOQueryRData)
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