[BioC] about refseq_dna in biomat
Hans-Rudolf Hotz
hrh at fmi.ch
Sat Oct 8 12:22:44 CEST 2011
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
>
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