Hi,
Thanks very much for your reply. Really useful, Andrea ________________________________ From: Vincent Carey <st...@channing.harvard.edu> Sent: 24 May 2017 17:20:48 To: Rodriguez Martinez, Andrea Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] getAnnMap: org.Hs.eg.db package not attached and load is FALSE That was an early approach to identifier mapping (ca. 2005 book), but things have changed a lot since then. Assuming you are dealing with human genes, you could use > select(Homo.sapiens, keys="5966", keytype="ENTREZID", columns="SYMBOL") 'select()' returned 1:1 mapping between keys and columns ENTREZID SYMBOL 1 5966 REL > mapIds(Homo.sapiens, keys="5966", keytype="ENTREZID", column="SYMBOL") 'select()' returned 1:1 mapping between keys and columns 5966 "REL" It is conceivable that one would want to use the ENSEMBL resource to do the same mapping, and it works too: > mapIds(EnsDb.Hsapiens.v75, keys="5966", keytype="ENTREZID", column="SYMBOL") 5966 "REL" The details of getting your approach to work with namespaces etc. I leave to others. On Wed, May 24, 2017 at 11:57 AM, Rodriguez Martinez, Andrea <andrea.rodriguez-martine...@imperial.ac.uk<mailto:andrea.rodriguez-martine...@imperial.ac.uk>> wrote: Hello, I wanted to use annotate to transform entrez IDs into symbols, inside my package. Something like for example: getSYMBOL("5966", data = 'org.Hs.eg<http://org.Hs.eg>') So I put in both NAMESPACE and description the annotate package and the org.Hs.eg.db package, but when I try to check my package and run the examples I get the following error: Error: getAnnMap: org.Hs.eg.db package not attached and load is FALSE Any help? Thanks very much, Andrea [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
