Updates the functions which list which genomes and gene IDs are suppo…

…rted. This change should make it clearer which are supported, rather than listing all possible genomes available in UCSC. Also adding Anthony Hawkins as a maintainer of the package.

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/geneLenDataBase@3686 db2202da-8704-0410-b924-b125b3cd84ef

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: geneLenDataBase
-Version: 1.7.0
-Date: 2010/03/30
+Version: 1.7.1
+Date: 2016/03/09
 Title: Lengths of mRNA transcripts for a number of genomes
 Author: Matthew Young
-Maintainer: Nadia Davidson <nadia.davidson@mcri.edu.au>
+Maintainer: Nadia Davidson <nadia.davidson@mcri.edu.au>, Anthony Hawkins <anthony.hawkins@mcri.edu.au>
 Depends: R (>= 2.11.0)
 Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15)
 LazyLoad: yes

R/supportedGeneIDs.R

@@ -1,7 +1,7 @@
 supportedGeneIDs=function(){
 	base=unfactor(GenomicFeatures:::supportedUCSCtables())
 	#Having the db entries as row names gets confusing, so fix that
-	base$db=rownames(base)
+ 	base$db=rownames(base)
 	base=base[,c(ncol(base),1:(ncol(base)-1))]
 	rownames(base)=1:nrow(base)
 	#Old version of GenomicFeatures
@@ -21,5 +21,7 @@ supportedGeneIDs=function(){
 	valid_genomes=sapply(split(repo[,1],repo[,2]),paste,collapse=",")
 	valid_genomes=valid_genomes[which(names(valid_genomes)%in%base$db)]
 	base$AvailableGenomes[match(names(valid_genomes),base$db)]=as.character(valid_genomes)
-	base
-}
+
+  avail = base[base$db == "knownGene" | base$db == "vegaGene" | base$db == "geneSymbol" | base$db == "ensGene",]
+  avail
+}

R/supportedGenomes.R

@@ -6,6 +6,6 @@ supportedGenomes=function(){
 	valid_ids=sapply(split(repo[,2],repo[,1]),paste,collapse=",")
 	valid_ids=valid_ids[which(names(valid_ids)%in%base$db)]
 	base$AvailableGeneIDs[match(names(valid_ids),base$db)]=as.character(valid_ids)
-	base
+	avail = base[base$AvailableGeneIDs != "",]
+	avail
 }
-