Hello, I'd like to ask you if there is an attribute for SNP function class for variation datasets in biomaRt that is equivalent to the field 'function-class' (or fxn-class field) in the dbSNP database (NCBI) and a related filter. I think biomaRt is great and I'd really like to use biomaRt to extract information on SNP function class such as synonymous-codon, nonsynonymous, non-genic. Any help will be appreciated. Thanks, Adriana On Wed, Nov 2, 2011 at 10:10 AM, <bioconductor-request@r-project.org> wrote: > Welcome to the Bioconductor@r-project.org mailing list! Welcome to the > Bioconductor mailing list. > > Please read the posting guide before sending your first post to the > list. > > http://www.bioconductor.org/docs/postingGuide.html > > > > To post to this list, send your message to: > > bioconductor@r-project.org > > General information about the mailing list is at: > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://stat.ethz.ch/mailman/options/bioconductor/adri.embo%40gmail .com > > > You can also make such adjustments via email by sending a message to: > > Bioconductor-request@r-project.org > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe without confirmation. It is: > > adriBio07 > > Normally, Mailman will remind you of your r-project.org mailing list > passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > [[alternative HTML version deleted]]

Hi Adriana, Please don't reply to the 'Welcome to the "Bioconductor" mailing list' email you received when you subscribed. There are many posts sent every day to this list and people don't have time to read them all: most of them decide to read or not a post based on its subject line. In your case this subject line will attract almost zero attention. On 11-11-02 07:17 AM, Adriana Munoz wrote: > Hello, > > I'd like to ask you if there is an attribute for SNP function class for > variation datasets in biomaRt that is equivalent to the field > 'function-class' (or fxn-class field) in the dbSNP database (NCBI) and > a related filter. I think biomaRt is great and I'd > really like to use biomaRt to extract information on SNP function class > such as synonymous-codon, nonsynonymous, non-genic. Which mart/dataset are you looking at? Did you try listAttributes()? Maybe an alternative to using biomaRt would be for you to have a look at the VariantAnnotation package (new in BioC 2.9). Cheers, H. > > Any help will be appreciated. > > Thanks, > > Adriana > > > On Wed, Nov 2, 2011 at 10:10 AM,<bioconductor-request at="" r-project.org=""> wrote: > >> Welcome to the Bioconductor at r-project.org mailing list! Welcome to the >> Bioconductor mailing list. >> >> Please read the posting guide before sending your first post to the >> list. >> >> http://www.bioconductor.org/docs/postingGuide.html >> >> >> >> To post to this list, send your message to: >> >> bioconductor at r-project.org >> >> General information about the mailing list is at: >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> If you ever want to unsubscribe or change your options (eg, switch to >> or from digest mode, change your password, etc.), visit your >> subscription page at: >> >> https://stat.ethz.ch/mailman/options/bioconductor/adri.embo%40gma il.com >> >> >> You can also make such adjustments via email by sending a message to: >> >> Bioconductor-request at r-project.org >> >> with the word `help' in the subject or body (don't include the >> quotes), and you will get back a message with instructions. >> >> You must know your password to change your options (including changing >> the password, itself) or to unsubscribe without confirmation. It is: >> >> adriBio07 >> >> Normally, Mailman will remind you of your r-project.org mailing list >> passwords once every month, although you can disable this if you >> prefer. This reminder will also include instructions on how to >> unsubscribe or change your account options. There is also a button on >> your options page that will email your current password to you. >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Adriana, by replying to the email you got when you subscribed, you just sent all of us (and those who may browse the archives) your password to the BioC list. Best, R. On Wed, 2 Nov 2011 10:17:37 -0400,Adriana Munoz <adri.embo at="" gmail.com=""> wrote: > Hello, > I'd like to ask you if there is an attribute for SNP function class for > variation datasets in biomaRt that is equivalent to the field > 'function-class' (or fxn-class field) in the dbSNP database (NCBI) and > a related filter. I think biomaRt is great and I'd > really like to use biomaRt to extract information on SNP function class > such as synonymous-codon, nonsynonymous, non-genic. > Any help will be appreciated. > Thanks, > Adriana > On Wed, Nov 2, 2011 at 10:10 AM, <bioconductor-request at="" r-project.org=""> wrote: > > Welcome to the Bioconductor at r-project.org mailing list! Welcome to the > > Bioconductor mailing list. > > > > Please read the posting guide before sending your first post to the > > list. > > > > http://www.bioconductor.org/docs/postingGuide.html > > > > > > > > To post to this list, send your message to: > > > > bioconductor at r-project.org > > > > General information about the mailing list is at: > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > If you ever want to unsubscribe or change your options (eg, switch to > > or from digest mode, change your password, etc.), visit your > > subscription page at: > > > > https://stat.ethz.ch/mailman/options/bioconductor/adri.embo%40gma il.com > > > > > > You can also make such adjustments via email by sending a message to: > > > > Bioconductor-request at r-project.org > > > > with the word `help' in the subject or body (don't include the > > quotes), and you will get back a message with instructions. > > > > You must know your password to change your options (including changing > > the password, itself) or to unsubscribe without confirmation. It is: > > > > adriBio07 > > > > Normally, Mailman will remind you of your r-project.org mailing list > > passwords once every month, although you can disable this if you > > prefer. This reminder will also include instructions on how to > > unsubscribe or change your account options. There is also a button on > > your options page that will email your current password to you. > > > [[alternative HTML version deleted]] > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25. Facultad de Medicina (UAM) Arzobispo Morcillo, 2 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz