[BioC] Querying dbSNP

[Vincent Carey]

if you add a function like this to your workspace, you can query on rs
number for some of the items you mention.  other retrieval approaches
could be based on NCBI eutils.

qsnp <- function (rsid, attrs = c("chr_name", "chrom_start", "allele",
    "associated_variant_risk_allele", "risk_allele_freq_in_controls",
    "allele_1", "associated_gene", "phenotype_description", "validated",
    "ensembl_peptide_shift"))
{
    if (!exists(".HSmart"))
        .HSmart <<- useMart(biomart = "snp", dataset = "hsapiens_snp")
    getBM(mart = .HSmart, filters = "refsnp", value = rsid, attributes = attrs)
}

> qsnp("rs13087941")
  chr_name chrom_start allele associated_variant_risk_allele
1        3     8787220    T/C                             NA
2        3     8787220    T/C                             NA
  risk_allele_freq_in_controls allele_1 associated_gene phenotype_description
1                           NA        C              NA                    NA
2                           NA        C              NA                    NA
                      validated ensembl_peptide_shift
1 cluster,freq,doublehit,hapmap                    NA
2 cluster,freq,doublehit,hapmap                 FALSE

be prepared for certain ambiguities to crop up

> qsnp("rs10000")
  chr_name chrom_start allele associated_variant_risk_allele
1        7     6013153    T/C                             NA
2        7     6013153    T/C                             NA
3        7     6790900    T/C                             NA
  risk_allele_freq_in_controls allele_1 associated_gene phenotype_description
1                           NA       NA              NA                    NA
2                           NA       NA              NA                    NA
3                           NA       NA              NA                    NA
     validated ensembl_peptide_shift
1 cluster,freq
2 cluster,freq                     L
3 cluster,freq


On Tue, Oct 20, 2009 at 5:11 AM, Sharon <sharonanandhi at gmail.com> wrote:
> Dear All,
>
> Thanks a lot for your suggestions. I did try with biomaRt to get CHR and POS
> info for SNPs. When I query dbSNP for a particular gene (Geneview report),
> we do get useful information such as validation, function and protein
> residue etc. for SNPs. Is it possible to get these information using
> biomaRt? If so, could you please tell me where can I find info for
> appropriate fields?
>
> Thanks again.
>
> Kind regards,
> Sharon
>
>
> On Mon, Oct 19, 2009 at 10:38 PM, <Steffen at stat.berkeley.edu> wrote:
>>
>> Also to note is that biomaRt indeed queries Ensembl for SNP queries and
>> these SNPs are from dbSNP mapped to Ensembl.
>>
>> The latest release notes from Ensembl 56 state:
>>
>> Ensembl variation mart 56
>>
>>    * Removal of Ensembl Celera, TSC and HGVBase information
>>    * Human now on dbSNP 130
>>
>>
>> Cheers,
>> Steffen
>>
>> > It may also be noteworthy that the SNPlocs.Hsapiens.dbSNP.20090506
>> > package has location and allele information for build 130 dbSNP
>> > entries. A substantial quantity of SNP-related metadata is present in
>> > the pd.genomewidesnp.6 annotation package.
>> >
>> >  'Queries' to dbSNP of a more general nature could probably be
>> > programmed using various web services support packages in R/bioc.  If
>> > you describe a compelling use case, code might be written to solve it.
>> >
>> > On Mon, Oct 19, 2009 at 4:30 PM, Marc Carlson <mcarlson at fhcrc.org>
>> > wrote:
>> >> Hi Sharon,
>> >>
>> >> It's not clear to me from your email what you intend to do, but I know
>> >> that some dbSNP data is available as a UCSC track and should therefore
>> >> be obtainable by using the rtracklayer package.
>> >>
>> >>  Marc
>> >>
>> >>
>> >> Sharon wrote:
>> >>> Dear All,
>> >>>
>> >>> Is there any tool in Bioconductor to query dbSNP? I know that (correct
>> >>> me,
>> >>> if I am wrong) biomaRt is primarily for Ensemble.
>> >>>
>> >>> Thanks in advance.
>> >>>
>> >>> Kind regards,
>> >>> Sharon.
>> >>>
>> >>>       [[alternative HTML version deleted]]
>> >>>
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>