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Question: about refseq_dna in biomat
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gravatar for Ou, Jianhong
6.3 years ago by
Ou, Jianhong1.0k
United States
Ou, Jianhong1.0k wrote:
dear list, I use biomaRt to get the genBank access id for some ensembl transcript ids. library(biomaRt) ensembl = useMart("ensembl") ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) access<-getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id",values=ensembl_t_ids,mart=ensembl) I got error, Error in getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id", : Invalid attribute(s): refseq_dna Please use the function 'listAttributes' to get valid attribute names What attributes should I use to instead "refseq_dna"? Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu
ADD COMMENTlink modified 6.3 years ago by Hotz, Hans-Rudolf390 • written 6.3 years ago by Ou, Jianhong1.0k
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gravatar for Hotz, Hans-Rudolf
6.3 years ago by
Switzerland
Hotz, Hans-Rudolf390 wrote:
Hi Are you interested in the GenBank accession (equal to EMBL accession) or the RefSeq accession? In any case you should follow the suggestion from the error message and look at 'listAttributes', and then you will find, among many others: 42 embl EMBL (Genbank) ID 74 ox_refseq_mrna__dm_dbprimary_acc_1074 RefSeq mRNA Hence: > library(biomaRt) > ensembl = useMart("ensembl") > ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) > getBM(attributes = "embl", filters = "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) embl 1 CH466529 2 BC129896 3 BC129897 4 AF039957 5 AB030729 > > getBM(attributes = "ox_refseq_mrna__dm_dbprimary_acc_1074", filters = "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) ox_refseq_mrna__dm_dbprimary_acc_1074 1 NM_019943 > Hope this helps. Regards, Hans > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.1 loaded via a namespace (and not attached): [1] RCurl_1.6-6 XML_3.4-0 > On 10/07/2011 07:22 PM, Ou, Jianhong wrote: > dear list, > > I use biomaRt to get the genBank access id for some ensembl transcript ids. > > library(biomaRt) > ensembl = useMart("ensembl") > ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) > access<-getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id",values=ensembl_t_ids,mart=ensembl) > > I got error, > Error in getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id", : > Invalid attribute(s): refseq_dna > Please use the function 'listAttributes' to get valid attribute names > > What attributes should I use to instead "refseq_dna"? > > Yours sincerely, > > Jianhong Ou > > jianhong.ou at umassmed.edu > > _______________________________________________ > 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 6.3 years ago by Hotz, Hans-Rudolf390
Thanks a lot. I got it. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Oct 8, 2011, at 6:22 AM, Hans-Rudolf Hotz wrote: > Hi > > Are you interested in the GenBank accession (equal to EMBL accession) or > the RefSeq accession? > > In any case you should follow the suggestion from the error message and > look at 'listAttributes', and then you will find, among many others: > > > 42 embl EMBL (Genbank) ID > > 74 ox_refseq_mrna__dm_dbprimary_acc_1074 RefSeq mRNA > > > Hence: > >> library(biomaRt) >> ensembl = useMart("ensembl") >> ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) >> getBM(attributes = "embl", filters = > "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) > embl > 1 CH466529 > 2 BC129896 > 3 BC129897 > 4 AF039957 > 5 AB030729 >> >> getBM(attributes = "ox_refseq_mrna__dm_dbprimary_acc_1074", filters = > "ensembl_transcript_id",values=c("ENSMUST00000099400"),mart=ensembl) > ox_refseq_mrna__dm_dbprimary_acc_1074 > 1 NM_019943 >> > > > > Hope this helps. > > Regards, Hans > > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-6 XML_3.4-0 >> > > > > > > > On 10/07/2011 07:22 PM, Ou, Jianhong wrote: >> dear list, >> >> I use biomaRt to get the genBank access id for some ensembl transcript ids. >> >> library(biomaRt) >> ensembl = useMart("ensembl") >> ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl) >> access<-getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id",values=ensembl_t_ids,mart=ensembl) >> >> I got error, >> Error in getBM(attributes = "refseq_dna", filters = "ensembl_transcript_id", : >> Invalid attribute(s): refseq_dna >> Please use the function 'listAttributes' to get valid attribute names >> >> What attributes should I use to instead "refseq_dna"? >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> _______________________________________________ >> 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 REPLYlink written 6.3 years ago by Ou, Jianhong1.0k
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