biomaRt: error using dataset from HapMap_rel27 mart
1
0
Entering edit mode
Brad McNeney ▴ 10
@brad-mcneney-4140
Last seen 9.6 years ago
Hello, I'm trying to use biomaRt to access SNP data from HapMap_rel27. > library(biomaRt) > hapmap<-useMart("HapMap_rel27") gives no trouble and I can list the available datasets. When I try to use any of the datasets I get the following: > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) Checking attributes ...Error in bmAttrFilt("attributes", mart) : biomaRt error: looks like we're connecting to incompatible version of BioMart suite. Can anyone suggest a work-around or error in what I'm doing? Or is it just not possible to access HapMap_rel27 with biomaRt? Session information included at the end of this message. Thanks, Brad --- Brad McNeney Statistics and Actuarial Science Simon Fraser University > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.4.0 loaded via a namespace (and not attached): [1] RCurl_1.4-2 tools_2.11.1 XML_3.1-0
SNP biomaRt SNP biomaRt • 1.1k views
ADD COMMENT
0
Entering edit mode
Steffen ▴ 500
@steffen-2351
Last seen 9.6 years ago
Hi Brad, I recently fixed this and it should work using the devel version of biomaRt which you can get from here: http://www.bioconductor.org/packages/2.7/bioc/html/biomaRt.html Using that version I get the following: > hapmap<-useMart("HapMap_rel27") > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) > listFilters(hapmap) name description 1 allele_freq Minor Allele Frequency [>=] 2 center Genotyping Center 3 platform Genotyping Platform 4 monomorphic Monomorphic SNPs 5 marker_name List of HapMap SNPs 6 utr3 3' UTR 7 utr5 5' UTR 8 coding_synon Exons - synonymous coding SNPs 9 coding_nonsynon Exons - non-synonymous coding SNPs 10 intronic introns 11 chrom chromosome 12 start From position 13 stop To position 14 gene_list List of Genes 15 encode_region ENCODE region > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.5.1 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 Cheers, Steffen On Thu, Jun 24, 2010 at 3:40 PM, Brad McNeney <mcneney@gmail.com> wrote: > Hello, > > I'm trying to use biomaRt to access SNP data from HapMap_rel27. > > > library(biomaRt) > > hapmap<-useMart("HapMap_rel27") > > gives no trouble and I can list the available datasets. When I try to > use any of the datasets I get the following: > > > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) > Checking attributes ...Error in bmAttrFilt("attributes", mart) : > biomaRt error: looks like we're connecting to incompatible version > of BioMart suite. > > Can anyone suggest a work-around or error in what I'm doing? Or is it > just not possible to access HapMap_rel27 with biomaRt? > > Session information included at the end of this message. > > Thanks, > > Brad > --- > Brad McNeney > Statistics and Actuarial Science > Simon Fraser University > > > > sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.4-2 tools_2.11.1 XML_3.1-0 > > _______________________________________________ > 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 COMMENT

Login before adding your answer.

Traffic: 739 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6