[BioC] getBM local

[steffen at stat.Berkeley.EDU]

Hi Amanda,

Unless your local source is not a BioMart database, you won't be able to
use getBM to query it.  If your local source is a copy of the BioMart
version of Ensembl, using the biomaRt package will work.  It should also
work if you have created your own BioMart database according to
http://www.biomart.org
However any other type of database schema won't work and to query that
you'll need to do as Mark suggested, use RMySQL or any of the other R
packages that enables you to do SQL queries to database systems.

Cheers,
Steffen

>
> Dear All
>
> I am looking to get getBM to read from a local source rather than ensembl.
> Would anyone have documentation or directions in relation to how to set
> this up?
>
> Thank you,
>
> Amanda Miotto
> a.miotto at griffith.edu.au
>
> Software Engineer.
> Research Computing Services
> INFORMATION SERVICES
> Griffith University, NATHAN 4111, AUSTRALIA
> Phone:  +61 7 37354419  Fax:  +61 7 37356650
> Web:    http://eResearch.griffith.edu.au/
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