UCSC changed some stuff

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/geneLenDataBase@3913 db2202da-8704-0410-b924-b125b3cd84ef

R/supportedGeneIDs.R

@@ -1,20 +1,21 @@
 supportedGeneIDs=function(){
 	base=unfactor(GenomicFeatures:::supportedUCSCtables())
-	#Having the db entries as row names gets confusing, so fix that
- 	base$db=rownames(base)
-	base=base[,c(ncol(base),1:(ncol(base)-1))]
-	rownames(base)=1:nrow(base)
-	#Old version of GenomicFeatures
-	#txname2gene_mapinfo=GenomicFeatures:::.UCSC_TXNAME2GENEID_MAPINFO
+
 	#Current version
 	txname2gene_mapinfo=GenomicFeatures:::.UCSC_TXNAME2GENEID_MAPDEFS
 	base$GeneID=""
+
 	#Old version
-	#tmp=unlist(sapply(txname2gene_mapinfo[base$db],function(u){u[4]}))
-	tmp=unlist(lapply(txname2gene_mapinfo[base$db],function(u){u[[2]]}))
-	base$GeneID[match(names(tmp),base$db)]=as.character(tmp)
+	#tmp=unlist(lapply(txname2gene_mapinfo[base$db],function(u){u[[2]]}))
+	#base$GeneID[match(names(tmp),base$db)]=as.character(tmp)
+
+	#NEW Ant 28/09/16
+	tmp=unlist(lapply(txname2gene_mapinfo[base$tablename],function(u){u[[2]]}))
+	base$GeneID = sapply(base$tablename,function(u){ifelse(u %in% names(tmp),tmp[u],"")})	
+	base$GeneID[match(names(tmp),base$tablename)]=as.character(tmp)
+
 	#Add in gene symbol
-	base[nrow(base)+1,]=c("geneSymbol",'refGene','refFlat',"Gene Symbol","")
+	base[nrow(base)+1,]=c("geneSymbol",'refGene','refFlat',"Gene Symbol")
 	base$AvailableGenomes=""
 	repo=grep(".*\\..*\\.LENGTH",as.data.frame(data(package="geneLenDataBase")$results,stringsAsFactors=FALSE)$Item,ignore.case=TRUE,value=TRUE)
 	repo=matrix(unlist(strsplit(repo,"\\.")),ncol=3,byrow=TRUE)