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.

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/ > > 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 >

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