Question: biomaRt and HapMap
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gravatar for Deidre
8.4 years ago by
Deidre10
Deidre10 wrote:
I need to get SNP data from HapMap via biomaRt, but am having trouble getting any results from any query of the hapmap_rel27 dataset. For example, both of the following: HM <- useMart("HapMap_rel27","hm27_variation_ceu") ceu <- getBM( c("chrom","start","strand","marker1"), filters=c("chrom"), values="chr22",HM) ) hapmap <- useMart("HapMap_rel27", dataset="hm27_variation_yri") yri <- getBM(c("chrom","start","alleles","ref_allele","ref_allele_freq","othe r_allele_freq",filters=c("chrom","coding_nonsynon"),values=list("chr19 ",TRUE),mart=hapmap) result in an empty table such as: > head(yri) [1] chrom start alleles ref_allele ref_allele_freq other_allele_freq <0 rows> (or 0-length row.names) I've tried with both biomaRt 2.8.1 and 2.9.2. Queries to marts ensembl or snp work as expected. Am I missing a detail in my queries to HapMap, or is there an issue with the mart? Regards, Deidre > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1251 LC_CTYPE=English_United States.1252 LC_MONETARY=English_united States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.9.2 loaded via a namespace (and not attached): [1] RCurl_1.6-6.1 tools_2.13.0 XML_3.4-0.2 [[alternative HTML version deleted]]
snp hapmap biomart • 876 views
ADD COMMENTlink modified 8.4 years ago by Steffen Durinck540 • written 8.4 years ago by Deidre10
Answer: biomaRt and HapMap
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gravatar for Steffen Durinck
8.4 years ago by
Steffen Durinck540 wrote:
Hi Deidre, It looks like there is some issue with HapMap in the BioMart central repository. You might want to do your query using the hapmap web interface at: http://hapmap.ncbi.nlm.nih.gov/biomart/martview/ Cheers, Steffen On Fri, Jul 22, 2011 at 5:58 AM, Deidre <deidre.krupp at="" duke.edu=""> wrote: > I need to get SNP data from HapMap via biomaRt, but am having trouble > getting any results from any query of the hapmap_rel27 dataset. ?For > example, both of the following: > > HM <- useMart("HapMap_rel27","hm27_variation_ceu") > ceu <- getBM( > c("chrom","start","strand","marker1"), > filters=c("chrom"), values="chr22",HM) > ) > > hapmap <- useMart("HapMap_rel27", dataset="hm27_variation_yri") > yri <- > getBM(c("chrom","start","alleles","ref_allele","ref_allele_freq","ot her_allele_freq",filters=c("chrom","coding_nonsynon"),values=list("chr 19",TRUE),mart=hapmap) > > result in an empty table such as: > > ?> head(yri) > [1] chrom ? ? ? ? ? ? start ? ? ? ? ? ? alleles > ref_allele ? ? ? ?ref_allele_freq ? other_allele_freq > <0 rows> (or 0-length row.names) > > I've tried with both biomaRt 2.8.1 and 2.9.2. ?Queries to marts ensembl > or snp work as expected. ?Am I missing a detail in my queries to HapMap, > or is there an issue with the mart? > > Regards, > Deidre > > > ?> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1251 ?LC_CTYPE=English_United > States.1252 ? ?LC_MONETARY=English_united States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United > States.1252 > > attached base packages: > [1] stats ? ?graphics ?grDevices utils ? ?datasets methods ?base > > other attached packages: > [1] biomaRt_2.9.2 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-6.1 tools_2.13.0 XML_3.4-0.2 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.4 years ago by Steffen Durinck540
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