Some developers have run into a new WARNING on the automatic package builder (bioc devel 3.1), specifically that org.Hs.egCHR is deprecated, and we should look to some other packages for transcript annotation.
A question was raised on the devel mailing list, How should we make these changes? They redirected us to this support site, but I don't see any discussion of the issue here, and that's the point of this new post.
I import org.Hs.eg.db to package rgsepd to make hashtables of lookups between RefSeq NM_## ids to their associated Entrez geneID and HGNC name. I don't directly use any of the sub-packages, org.Hs.egCHR , org.Hs.egCHRLENGTHS , org.Hs.egCHRLOC , org.Hs.egCHRLOCEND which are deprecated and causing the warning.
I just need an ID conversion table, and when looking at things like TxDb.Hsapiens.UCSC.hg19.knownGene; no information is given on usage. The man pages are empty at http://www.bioconductor.org/packages/devel/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html
So I need to ask the community how do we use these TxDBs, what is the minimal data I can IMPORT to my package for a comprehensive ID conversion? I do mRNA and ncRNA, so I might need TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts as well, but again the man pages are empty!
I know we can use bioMart for some lookups, but as I do a lot of repeated querying, an offline database seems the more efficient solution.