diff Analyse.R @ 2:93451f832736 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Analyse.R	Tue Mar 21 10:28:47 2017 -0400
@@ -0,0 +1,145 @@
+library(Biobase)
+library(GEOquery)
+library(GEOmetadb)
+library(limma)
+library(jsonlite)
+library(affy)
+library(dplyr)
+
+cargs<-commandArgs()
+cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
+nbargs=length(cargs)
+
+load(cargs[[nbargs-13]])
+targetFile=cargs[[nbargs-12]]
+condition1Name=cargs[[nbargs-11]]
+condition1=cargs[[nbargs-10]]
+condition2Name=cargs[[nbargs-9]]
+condition2=cargs[[nbargs-8]]
+nbresult=cargs[[nbargs-7]]
+result_export_eset=cargs[[nbargs-6]]
+result=cargs[[nbargs-5]]
+result.path=cargs[[nbargs-4]]
+result.tabular=cargs[[nbargs-3]]
+result.template=cargs[[nbargs-2]]
+
+#file.copy(targetFile,"./targetFile.txt")
+
+condition1_tmp <- strsplit(condition1,",")
+condition1 <-unlist(condition1_tmp)
+
+condition2_tmp <- strsplit(condition2,",")
+condition2<-unlist(condition2_tmp)
+
+conditions=c(condition1,condition2)
+
+#nbresult=1000
+dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
+
+targets <- read.table(targetFile,sep="\t")
+
+eset=eset[,which(rownames(eset@phenoData@data) %in% conditions)]
+#condition1Name=make.names(condition1Name)
+#condition2Name=make.names(condition2Name)
+#condition1Name=gsub("_","",condition1Name)
+#condition2Name=gsub("_","",condition2Name)
+#condition1Name
+#condition2Name
+
+
+eset@phenoData@data$source_name_ch1=""
+eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition1)]=condition1Name
+eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition2)]=condition2Name
+#condition1Name
+#condition2Name
+
+condNames=paste0("G",as.numeric(as.character(pData(eset)["source_name_ch1"][,1])!=condition1Name))
+#condNames=make.names(targets[,2])
+#condNames=gsub("_","",condNames)
+
+f <- as.factor(condNames)
+#eset$description <- factors
+design <- model.matrix(~ 0+f)
+design
+
+colnames(design) <- levels(f)
+colnames(design)
+fit <- lmFit(eset, design)
+fit
+#cont.matrix <- makeContrasts(C1=paste0(condition1Name,"-",condition2Name), levels=design)
+cont.matrix <- makeContrasts(G0-G1, levels=design)
+cont.matrix
+fit2 <- contrasts.fit(fit, cont.matrix)
+fit2 <- eBayes(fit2)
+fit2
+tT <- topTable(fit2, adjust="fdr", sort.by="B", number=nbresult)
+
+#head(exprs(eset))
+
+gpl <- annotation(eset)
+if (substr(x = gpl,1,3)!="GPL"){
+	#if the annotation info does not start with "GPL" we retrieve the correspondin GPL annotation
+	mapping=read.csv("/galaxy-tools/transcriptomics/db/gplToBioc.csv",stringsAsFactors=FALSE)
+	gpl=mapping[which(mapping$bioc_package==annotation(eset)),]$gpl
+	gpl=gpl[1]
+	
+	annotation(eset)=gpl
+	
+	platf <- getGEO(gpl, AnnotGPL=TRUE)
+	ncbifd <- data.frame(attr(dataTable(platf), "table"))
+	
+	fData(eset)["ID"]=row.names(fData(eset))
+	fData(eset)=merge(x=fData(eset),y=ncbifd,all.x = TRUE, by = "ID")
+	colnames(fData(eset))[4]="ENTREZ_GENE_ID"
+	row.names(fData(eset))=fData(eset)[,"ID"]
+	
+	tT <- add_rownames(tT, "ID")
+	
+} else {
+	
+	gpl <- annotation(eset)
+	platf <- getGEO(gpl, AnnotGPL=TRUE)
+	ncbifd <- data.frame(attr(dataTable(platf), "table"))
+	
+	if (!("ID" %in% colnames(tT))){
+		tT <- add_rownames(tT, "ID")}
+	
+}
+
+tT <- merge(tT, ncbifd, by="ID")
+tT <- tT[order(tT$P.Value), ] 
+tT <- subset(tT, select=c("Platform_SPOTID","ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title","Gene.ID","Chromosome.annotation","GO.Function.ID"))
+tT<-format(tT, digits=2, nsmall=2)
+head(tT)
+colnames(tT)=gsub(pattern = "\\.",replacement = "_",colnames(tT))
+matrixtT=as.matrix(tT)
+datajson=toJSON(matrixtT,pretty = TRUE)
+
+htmlfile=readChar(result.template, file.info(result.template)$size)
+htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
+dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
+
+boxplot="boxplot.png"
+png(boxplot,width=800,height = 400)
+par(mar=c(7,5,1,1))
+boxplot(exprs(eset),las=2,outline=FALSE)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
+file.copy(boxplot,result.path)
+
+histopvalue="histopvalue.png"
+
+png(histopvalue,width=800,height = 400)
+par(mfrow=c(1,2))
+hist(fit2$F.p.value,nclass=100,main="Histogram of p-values", xlab="p-values",ylab="frequency")
+volcanoplot(fit2,coef=1,highlight=10,main="Volcano plot")
+htmlfile=gsub(x=htmlfile,pattern = "###HIST###",replacement = histopvalue, fixed = TRUE)
+dev.off()
+file.copy(histopvalue,result.path)
+
+#write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
+saveConditions=c(condition1Name,condition2Name)
+save(eset,saveConditions,file=result_export_eset)
+write.table(x=tT[,-1],file=result.tabular,quote=FALSE,row.names=FALSE,col.names=TRUE,sep="\t")
+write(htmlfile,result)
+