[BioC] about refseq_dna in biomat

[Ou, Jianhong]

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