[BioC] Querying dbSNP
Steffen at stat.Berkeley.EDU
Steffen at stat.Berkeley.EDU
Tue Oct 20 23:51:30 CEST 2009
Hi Sharon,
Can you give the exact query you were performing? This is not a desired
error and has to do with a feature of the SNP BioMart that needs to be
resolved. The error might go away by removing a specific attribute from
your query.
Cheers,
Steffen
> Dear Vincent,
>
> Though I get required info, I do get the following error message:
>
> Error in getBM(mart = .gmart, filters = "hgnc_symbol", value = gname, :
> The query to the BioMart webservice returned an invalid result: the
> number
> of columns in the result table does not equal the number of attributes in
> the query. Please report this to the mailing list.
>
> Do I need to consider this seriously?
>
> Thanks again,
> Sharon
>
> On Tue, Oct 20, 2009 at 12:12 PM, Vincent Carey
> <stvjc at channing.harvard.edu>wrote:
>
>> 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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