[BioC] about refseq_dna in biomat

[Hans-Rudolf Hotz]

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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