[BioC] getBM local

steffen at stat.Berkeley.EDU steffen at stat.Berkeley.EDU
Fri Jul 25 17:55:45 CEST 2008

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
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.


> 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
> Griffith University, NATHAN 4111, AUSTRALIA
> Phone:  +61 7 37354419  Fax:  +61 7 37356650
> Web:    http://eResearch.griffith.edu.au/
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