[BioC] about refseq_dna in biomat
Ou, Jianhong
Jianhong.Ou at umassmed.edu
Sat Oct 8 14:16:53 CEST 2011
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
>>
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