[BioC] Welcome to the "Bioconductor" mailing list

Hervé Pagès hpages at fhcrc.org
Wed Nov 2 18:25:37 CET 2011

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).


> 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%40gmail.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

More information about the Bioconductor mailing list