biomaRt: how to retrieve the MOUSE gene symbol?
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 3 days ago
Wageningen University, Wageningen, the …
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@james-w-macdonald-5106
Last seen 1 day ago
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Hi Guido, Hooiveld, Guido wrote: > Dear list, > > Likely an easy question, but can someone plz inform me how to > retrieve the MOUSE gene symbol using biomaRt? For human you can use > as attribute "hgnc_symbol", and for mouse genes I also would like to > have the gene symbol returned. I do know this property is present at > Ensembl as MGI Symbol, but when listing the filters for Mouse I don't > find this entry. > getBM("markersymbol", "affy_mouse430_2", "1415670_at", mart) markersymbol 1 Copg Best, Jim > > Thanks, Guido > > My code: [Note: I do know why I get the error; that's because I am > querying mouse and not human, and the attribute hgnc_symbol does not > exist in mmusculus_gene_ensembl. The question is which attribute to > use for mouse?]. > > >> library(biomaRt) > Loading required package: XML Loading required package: RCurl Warning > message: package 'biomaRt' was built under R version 2.6.0 >> ensembl = useMart("ensembl") ensembl = >> useDataset("mmusculus_gene_ensembl",mart=ensembl) > Checking attributes and filters ... ok >> # to check which information is available that can be retrieved: >> filters = listFilters(ensembl) filters > name description 1 > affy_mg_u74a Affy mg u74a ID(s) 2 > affy_mg_u74av2 Affy mg u74av2 ID(s) 3 > affy_mg_u74b Affy mg u74b ID(s) 4 > affy_mg_u74bv2 Affy mg u74bv2 ID(s) Etc. <snip> > by me >> e <- getBM(attributes=c("uniprot_swissprot_accession", >> "uniprot_swissprot", "hgnc_symbol", "entrezgene", >> "ensembl_transcript_id"), filter="uniprot_swissprot_accession", >> values=swissprot_ids, mart=ensembl) > Error in getBM(attributes = c("uniprot_swissprot_accession", > "uniprot_swissprot", : Invalid attribute(s): hgnc_symbol Please use > the function 'listAttributes' to get valid attribute names >> sessionInfo() > R version 2.5.0 (2007-04-23) i386-pc-mingw32 > > locale: LC_COLLATE=English_United > Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: [1] "stats" "graphics" "grDevices" > "utils" "datasets" "methods" [7] "base" > > other attached packages: biomaRt RCurl XML "1.11.3" "0.8-0" > "1.7-3" > > > > > ------------------------------------------------ Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group Division of Human Nutrition > Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen > the Netherlands > > tel: (+)31 317 485788 fax: (+)31 317 483342 > > internet: http://nutrigene.4t.com email: guido.hooiveld at wur.nl > > > > [[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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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