Question: Querying dbSNP
0
gravatar for Sharon Anbu
10.0 years ago by
Sharon Anbu480
Sharon Anbu480 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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ADD COMMENTlink modified 10.0 years ago by Marc Carlson7.2k • written 10.0 years ago by Sharon Anbu480
Answer: Querying dbSNP
0
gravatar for Marc Carlson
10.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 10.0 years ago by Marc Carlson7.2k
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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.0 years ago by Vincent J. Carey, Jr.6.3k
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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.0 years ago by steffen@stat.Berkeley.EDU600
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]]
ADD REPLYlink written 10.0 years ago by Sharon Anbu480
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]] >> >>> >> >>> _______________________________________________ >> >>> Bioconductor mailing list >> >>> Bioconductor at 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 at 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 at 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 at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 10.0 years ago by Vincent J. Carey, Jr.6.3k
Dear Vincent, Thank you very much. Your suggestions helped me a lot to retrieve SNPs for a set of genes. I am specifically interested in getting 'consequence_type' attributes. 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]]
ADD REPLYlink written 10.0 years ago by Sharon Anbu480
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]]
ADD REPLYlink written 10.0 years ago by Sharon Anbu480
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]] >> >> >>> >> >> >>> _______________________________________________ >> >> >>> Bioconductor mailing list >> >> >>> Bioconductor at 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 at 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 at 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 at 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.0 years ago by steffen@stat.Berkeley.EDU600
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]]
ADD REPLYlink written 10.0 years ago by Sharon Anbu480
HI Sharon, why not consumer their web-service in a Perl script with SOAP? You can pipe data to R from Perl to perform any analytics that you may need. Cheers! - SanjaY Marc Carlson 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 [1]Bioconductor at stat.math.ethz.ch [2]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [3]http://news.gmane.org/gmane.science.biology.informatics .conductor _______________________________________________ Bioconductor mailing list [4]Bioconductor at stat.math.ethz.ch [5]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [6]http://news.gmane.org/gmane.science.biology.informatics .conductor References 1. mailto:Bioconductor at stat.math.ethz.ch 2. https://stat.ethz.ch/mailman/listinfo/bioconductor 3. http://news.gmane.org/gmane.science.biology.informatics.conductor 4. mailto:Bioconductor at stat.math.ethz.ch 5. https://stat.ethz.ch/mailman/listinfo/bioconductor 6. http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.0 years ago by Dr. Sanjay Bhatikar30
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