Hi Steffen, I thought of getting Ensemble IDs for my genes before I extract SNPs. So, I have used: ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") getBM(attributes = c("hgnc_symbol","ensembl_gene_id","entrezgene", "chromosome_name", "start_position", "end_position"), filters="hgnc_symbol", values=gene, mart = ensembl) Is this because I am using an old version of R (2.9.0)? Thanks, Sharon sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.95-1 XML_2.3-0 On Tue, Oct 20, 2009 at 10:51 PM, <steffen@stat.berkeley.edu> wrote: > 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@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@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@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@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]] > >> >> >>> > >> >> >>> _______________________________________________ > >> >> >>> Bioconductor mailing list > >> >> >>> Bioconductor@stat.math.ethz.ch > >> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> >>> Search the archives: > >> >> >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> >>> > >> >> >>> > >> >> >> > >> >> >> _______________________________________________ > >> >> >> Bioconductor mailing list > >> >> >> Bioconductor@stat.math.ethz.ch > >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> >> Search the archives: > >> >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> >> > >> >> > > >> >> > _______________________________________________ > >> >> > Bioconductor mailing list > >> >> > Bioconductor@stat.math.ethz.ch > >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> > Search the archives: > >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@stat.math.ethz.ch > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: > >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > >> > > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]