It might also be helpful to try a dry-run on the martview website to learn about the different possible attributes and filters and try some queries. The display names of the controls on the page are identical to the discription field given when using listAttributes or listFilters For example, your query might look very much like the following link: http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTR IBUTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr _name|hsapiens_snp.default.snp.chrom_start|hsapiens_snp.default.snp.al lele|hsapiens_snp.default.snp.associated_gene|hsapiens_snp.default.snp .ensembl_gene_stable_id|hsapiens_snp.default.snp.ensembl_transcript_st able_id&FILTERS=hsapiens_snp.default.filters.refsnp."rs6494144"&VISIBL EPANEL=resultspanel Best Michael Am Dec 17, 2009 um 4:40 PM schrieb Vincent Carey: > try the code that i provided and then look more closely at the allatt vector > to see the kinds of information you can obtain from biomaRt calls. you will > need to install biomaRt in a current version of R, use biocLite. > > On Thu, Dec 17, 2009 at 10:25 AM, Peter Ganske <peter.ganske at="" hki-="" jena.de="">wrote: > >> Hello everybody, >> sorry for the question. Right, it was not very well-posed. >> Well: I need information about the SNPs. For example: >> >> I have SNP rs6494144 and i want to get informations about the position, the >> allele and if this SNP occour in genes. >> >> I want to generate a gene list for checking the generated list with an list >> i got from a previous paper. I saw that there is the possibility to work >> with PLINK for generating a SNP list with an gene list as the input. So I >> want to do this vice versa. >> Hope, that my question is clearer now. >> Thanks for the help >> >> Peter >> >> >> >> >> >> >>>>> Vincent Carey <stvjc at="" channing.harvard.edu=""> 17.12.2009 15:47 >>> >> >> the question is not very well-posed, but you can do something along >> these lines with biomaRt >> >> mart = useMart("snp") >> ds = useMart("snp", data="hsapiens_snp") >> allatt = listAttributes(ds)[,1] >> allfilt = listFilters(ds)[,1] >> getBM(allatt[c(1:5,9,59,60)], filters="refsnp", values="rs206116", mart=ds) >> >> indeed the question of what 'association' between SNP and gene is of >> concern needs to be made much clearer. if you are interested in the >> eQTL concept, the GGtools package has relevant tools and example data. >> >> >> On Thu, Dec 17, 2009 at 9:27 AM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> wrote: >>> Hi Peter, >>> >>> Peter Ganske wrote: >>>> >>>> Hello everybody, i got a list of SNPs. Is there a package to get >>>> informations about the association with genes automatically? I want >>>> to check the SNPs and collect some informations about them. Would be >>>> amazing, if anybody can help me out. Thanks in advance Peter >>> >>> Not that I know of. And certainly not something that you can plug in a >> bunch >>> of rs numbers and automagically get all kinds of info returned. >>> >>> Any response depends on what you mean by 'association with genes'. If you >>> mean something naive like 'is this SNP between the 5' and 3' UTR of some >>> gene, then you could use the org.Xx.eg.db package for your organism along >>> with the IRanges package to find SNPs that are 'in' genes. >>> >>> Anything more sophisticated than that will likely require you to write >> your >>> own functions and/or use software outside the Bioconductor project. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> >>>> >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the original >>>> message from your mail system. [[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.conducto r<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >> be >>> used for urgent or sensitive issues >>> _______________________________________________ >>> 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 >>> >> The information contained in this email and any attachments is confidential >> and may be subject to copyright or other intellectual property protection. >> If you are not the intended recipient, you are not authorized to use or >> disclose this information, and we request that you notify us by reply mail >> or telephone and delete the original message from your mail system. >> > > [[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