Nothing
checkUpdates <- function(con,GSEid=NULL){
gseData <- GSEinDB(con,GSEid)
dir <- path.package("compendiumdb")
scriptLoc <- paste(dir,"/scripts/R/downloadSoftFile.R",sep="")
scriptLoc <- gsub("^","\"",scriptLoc)
scriptLoc <- gsub("$","\"",scriptLoc)
# Download soft file from GEO and retrieve the last updated date
updateDates <- unlist(lapply(unique(gseData$Experiment),function(x){
system(paste("Rscript",scriptLoc,x,"gse.new 0",sep=" "))
data=read.delim("gse.new.soft",sep="=",header=F)
c(x,as.character(data[data[,1]=="!Series_last_update_date ",2]))
}))
updateDates <- matrix(updateDates,ncol=2,byrow=T)
updateDates <- as.data.frame(updateDates)
colnames(updateDates)=c("Experiment","LastUpdateDate")
result <- unique(merge(updateDates,gseData[,c("Experiment","DateLoaded")],by="Experiment"))
diff <- as.numeric(as.Date(gsub(" .*","",result$DateLoaded),"%Y-%m-%d")-as.Date(result$LastUpdateDate," %b %d %Y"))
## GSEs updated on GEO
fRes <- result[which(ifelse(sign(diff)<0,TRUE,FALSE)),]
if (nrow(fRes)==0){
cat("None of the specified GSEs loaded in the compendium database have been updated on GEO\n")
}else{
rownames(fRes) <- 1:nrow(fRes)
fRes
}
}
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