[Bioc-devel] getAnnMap: org.Hs.eg.db package not attached and load is FALSE

[Rodriguez Martinez, Andrea]

Hi,


Thanks very much for your reply.  Really useful,


Andrea

________________________________
From: Vincent Carey <stvjc at channing.harvard.edu>
Sent: 24 May 2017 17:20:48
To: Rodriguez Martinez, Andrea
Cc: bioc-devel at 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-martinez13 at imperial.ac.uk<mailto:andrea.rodriguez-martinez13 at 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

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