[BioC] biomRt package to get the 3'utr sequences of refseq predicted genes

[steffen at stat.Berkeley.EDU]

Hi Harpreet,

Thanks for reporting this.  getSequence is a wrapper function that makes
thing easy to retrieve but it expect certain things such as that the used
filter is also an attribute that is retrievable.  In this case
refseq_dna_predicted is given as filter but the corresponding attribute is
refseq_DNA_predicted so these are not the same and this makes your query
fail.  I'll investigate this mismatch and try to fix it.  In the meantime
you could do your query:

getBM(c("ensembl_gene_id","3utr"), filters= "refseq_dna_predicted", values
= "XM_940223", mart = ensembl)

This should work.

Cheers,
Steffen


> Hi,
>
> I am getting some problem in using 'BiomaRt' package to obtain the 3'
> UTR sequences of refseq predicted genes. I am using the following
> command:
>  >
> getSequence
> (id=refseqID,type="refseq_dna_predicted",seqType="3utr",mart=ensembl),
> where refseqId is a list of my refseq predicted genes.
>
> I am getting the following error:
>
> Error in getBM(c(seqType, type), filters = type, values = id, mart =
> mart,  :
>    Invalid attribute(s): refseq_dna_predicted
>
> I checked the filters and attributes also to confirm if the type is
> alright. It seems that the type should be 'refseq_dna_predicted'.
>
> Any help would be great.
>
> sessionInfo()
>  > sessionInfo()
> R version 2.7.2 (2008-08-25)
> i386-apple-darwin8.11.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GEOquery_2.4.5 Biobase_2.0.1  limma_2.14.6   biomaRt_1.14.1
> RCurl_0.9-4
>
> loaded via a namespace (and not attached):
> [1] XML_1.96-0
>
>
> Thanks
> Harpreet
> Harpreet Kaur Saini
> Enright Group
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD
> Tel: +44-(0) 1223-492676
>
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