[BioC] problem getting biotype in biomaRt

[steffen at stat.Berkeley.EDU]

Hi Elizabeth,

The biotype attribute seem to have changed into a separate gene_biotype
and transcript_biotype  these two represent the same info.

These two new attributes however are indeed currently not retrievable and
I am investigating what causes this. It looks like it is on the BioMart
side.

Cheers,
Steffen



> Hi,
> I am trying to pull down information from Ensembl using biomaRt and I
> can't get the relevant biotype information (for Human). The old
> 'biotype' attribute doesn't exist, so what I see is 'gene_biotype' and
> 'structure_biotype'. I have no idea what the difference is, but I can't
> get either one. The error says it's probably an internal error to be
> reported, but I also get this when I try to bring down what I think are
> incompatible attributes.
> Thanks,
> Elizabeth
>
>  > library(biomaRt)
>  > mart<-useMart("ensembl",dataset= "hsapiens_gene_ensembl")
> Checking attributes and filters ... ok
>  > martAttr<-listAttributes(mart)
>  > att<-c("ensembl_gene_id",
> +                 "ensembl_transcript_id",
> +                 "ensembl_exon_id",
> +                  "exon_chrom_start",
> +                  "exon_chrom_end",
> +                  "strand",
> +                  "chromosome_name",
> +                  "rank",
> +                  "3_utr_start","3_utr_end",
> +                  "5_utr_start","5_utr_end"
> +                  )
>  > all(att%in%martAttr[,1]) #valid names for the mart
> [1] TRUE
> #works fine here
>  > tempGene <-
> getBM(att,filter="ensembl_gene_id",value="ENSG00000187634",mart = mart)
> #error
>  > tempGene <-
> getBM(c(att,"gene_biotype"),filter="ensembl_gene_id",value="ENSG00000187634",mart
> = mart)
>
>                                  V1
> 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from
> multiple attribute pages are not allowed
> Error in getBM(c(att, "gene_biotype"), filter = "ensembl_gene_id", value
> = "ENSG00000187634",  :
>    Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please report.
> #again an error
>  > tempGene <-
> getBM(c(att,"structure_biotype"),filter="ensembl_gene_id",value="ENSG00000187634",mart
> = mart)
>
>     V1
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype NOT
> FOUND
> Error in getBM(c(att, "structure_biotype"), filter = "ensembl_gene_id",  :
>    Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please report.
>  > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_1.16.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.93-0 tools_2.8.1  XML_1.99-0
>
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