[BioC] getBM local

[Mark Robinson]

Hi Amanda.

According to the 'getBM' example, you need to call 'useMart' to setup  
the connection.  Presumably, you could direct 'useMart' to your local  
DB via its web service or mysql.  A place to start is '?useMart'.  I'm  
not sure how Biomart-like in terms of schemas your local DB will need  
to be in order to use getBM.  Looking at the source for 'getBM' might  
help there.


 >      mart <- useMart("ensembl")
 >      datasets <- listDatasets(mart)
 >      mart<-useDataset("hsapiens_gene_ensembl",mart)
Checking attributes and filters ... ok
 >      v<- 
getBM 
(attributes 
= 
c 
("affy_hg_u95av2 
","hgnc_symbol 
","chromosome_name 
","band 
"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"),  
mart=mart)
  affy_hg_u95av2 hgnc_symbol chromosome_name   band
1        1454_at       SMAD3              15 q22.33
2        1503_at       BRCA2              13  q13.1
3        1503_at                          13  q13.1
4        1939_at        TP53              17  p13.1
 > class(v)
[1] "data.frame"

 > mart
Object of class 'Mart':
Using the ensembl BioMart database
Using the hsapiens_gene_ensembl dataset
 > slotNames(mart)
[1] "mysql"            "connections"      "mysqldriver"       
"mainTables"
[5] "biomart"          "host"             "port"             "vschema"
[9] "dataset"          "filters"          "attributes"        
"attributePointer"
[13] "archive"
 > mart at host
[1] "http://www.biomart.org:80/biomart/martservice"
 > mart at mysql
[1] FALSE


Alternatively (and I'm not sure exactly what need downstream of this),  
since 'getBM' simply returns a data frame, perhaps just a simple query  
to your database (e.g. dbSendQuery and fetch from RMySQL) that returns  
a table would be just as simple.  (Sorry, this is the same answer I  
gave in your previous question).

Mark



On 25/07/2008, at 11:50 AM, Amanda Miotto wrote:

>
> 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/
>
> PRIVILEGED - PRIVATE AND CONFIDENTIAL:
> This email and any files transmitted with it are intended solely for
> the use of the addressee(s) and may contain information which is
> confidential or privileged.  If you receive this email and you are
> not the addressee(s) [or responsible for delivery of the email to the
> addressee(s)], please disregard the contents of the email, delete the
> email and notify the author immediately.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852