getBM function in biomaRt
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I wanted to get some exon information for specific genes. I wanted to use the hg17 build, since my SNP data is based on that. The code that I use is: ------------------------------------- library(biomaRt) entrezid <- "8334" martx <- "ensembl_mart_49" ensembl <- useMart(biomart=martx,dataset="hsapiens_gene_ensembl", archive=TRUE) ### "ensembl_mart_49" hg17 for wtccc zz <- getBM(attr = c("entrezgene","exon_stable_id", "exon_chrom_start","exon_chrom_end"), filters="with_entrezgene", values = entrezid,mart = ensembl) ------------------------------------ However, I get the following error: Error in listFilters(mart, what = "type") : The function argument 'what' contains an invalid value: type Valid are: name, description, options, fullDescription, filters5, filters6 I checked with listFilters(ensembl) and ?getBM, and the filters appear to be ok. What am I doing wrong? thanks! My sessionInfo(): R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] GOstats_2.12.0 graph_1.24.1 Category_2.12.0 [4] GO.db_2.3.5 multtest_2.2.0 XML_2.6-0 [7] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 [10] AnnotationDbi_1.8.0 GEOquery_2.8.0 RCurl_1.2-1 [13] bitops_1.0-4.1 biomaRt_2.2.0 DBI_0.2-4 [16] RColorBrewer_1.0-2 genefilter_1.28.0 affy_1.24.1 [19] Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 [3] GSEABase_1.8.0 MASS_7.3-3 [5] preprocessCore_1.8.0 RBGL_1.20.0 [7] splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 xtable_1.5-6 > [[alternative HTML version deleted]]
SNP GO hgu133a SNP GO hgu133a • 1.4k views
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@steffenstatberkeleyedu-2907
Last seen 7.9 years ago
Hi Tim, biomaRt works with archives from about Ensembl version 52 and upwards. Hg17 corresponds to NCBI35 which is in Ensembl 35, you'll need to get a very old archive. You could get the data you need via the web BioMart interface: http://nov2005.archive.ensembl.org/index.html follow the BioMart link to make a query. Hope this helps, Steffen > Hi, > > I wanted to get some exon information for specific genes. I wanted to use > the hg17 build, since my SNP data is based on that. The code that I use > is: > ------------------------------------- > library(biomaRt) > entrezid <- "8334" > martx <- "ensembl_mart_49" > > ensembl <- useMart(biomart=martx,dataset="hsapiens_gene_ensembl", > archive=TRUE) ### "ensembl_mart_49" hg17 for wtccc > zz <- getBM(attr = c("entrezgene","exon_stable_id", > "exon_chrom_start","exon_chrom_end"), > filters="with_entrezgene", > values = entrezid,mart = ensembl) > > > ------------------------------------ > However, I get the following error: > Error in listFilters(mart, what = "type") : > The function argument 'what' contains an invalid value: type > Valid are: name, description, options, fullDescription, filters5, filters6 > > I checked with listFilters(ensembl) and ?getBM, and the filters appear to > be ok. What am I doing wrong? > thanks! > My sessionInfo(): > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > other attached packages: > [1] GOstats_2.12.0 graph_1.24.1 Category_2.12.0 > [4] GO.db_2.3.5 multtest_2.2.0 XML_2.6-0 > [7] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [10] AnnotationDbi_1.8.0 GEOquery_2.8.0 RCurl_1.2-1 > [13] bitops_1.0-4.1 biomaRt_2.2.0 DBI_0.2-4 > [16] RColorBrewer_1.0-2 genefilter_1.28.0 affy_1.24.1 > [19] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 > [3] GSEABase_1.8.0 MASS_7.3-3 > [5] preprocessCore_1.8.0 RBGL_1.20.0 > [7] splines_2.10.0 survival_2.35-7 > [9] tools_2.10.0 xtable_1.5-6 >> > > > > [[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 >
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