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

[Vincent Carey]

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> 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')
>
>
> 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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