[BioC] Error using makeGeneRegion/getBM/listFilters, argument 'what' contains an invalid value: type

[Steffen at stat.Berkeley.EDU]

Hi Tejal,

Ensembl 46 is to old and there have been some major changes since for
biomaRt to work with it.  Would a more recent ensembl archive work for
you?
For example Ensembl 54 is NCBI36 and might be what you were looking for
unless you have another reason to specifically want Ensembl 46?
You can access Ensembl 54 like this:

> listMarts(host="may2009.archive.ensembl.org/biomart/martservice")
               biomart              version
1 ENSEMBL_MART_ENSEMBL           Ensembl 54
2     ENSEMBL_MART_SNP Ensembl Variation 54
3    ENSEMBL_MART_VEGA              Vega 35
4             REACTOME   Reactome(CSHL US)
5     wormbase_current   WormBase (CSHL US)
6                pride       PRIDE (EBI UK)
> ens54 = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl"
,host="may2009.archive.ensembl.org/biomart/martservice")
Checking attributes and filters ... ok



Cheers,
Steffen



> Hi,
> I have been trying to work with an archived version of ensembl mart, i.e.
> ensembl_46. The code goes as follow:
>
>>library(biomaRt)
>>#listMarts(archive=TRUE)
>>mart=useMart("ensembl_mart_46", archive=TRUE)
>>## listDatasets(mart)
>>mart=useDataset("mmusculus_gene_ensembl",mart)
> Checking attributes ... ok
> Checking filters ... ok
> Warning messages:
> 1: In bmAttrFilt("attributes", mart) :
>   biomaRt warning: looks like we're connecting to an older version of
> BioMart suite. Some biomaRt functions might not work.
> 2: In bmAttrFilt("filters", mart) :
>   biomaRt warning: looks like we're connecting to an older version of
> BioMart suite. Some biomaRt functions might not work.
>
>> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end
>> =
> 30550000, strand = "+", biomart = mart)
>
>
> I have modified the GeneRegion method such that it can work with older,
> hardcoded attribute names. It started to give error once again due to
> "strand" not being one of the filters supported by old ensembl build.
> Therefore, I tried a simpler way to collect genomic features from biomart
> :
>
>  > getBM(c("gene_stable_id","transcript_stable_id",
>
> "exon_stable_id","exon_chrom_start","exon_chrom_end",
>                                 "rank",
> "transcript_chrom_strand","struct_biotype"),
>
> filters=c("chromosome_name","start","end"),values=list(17,30450000,30455000),mart)
>
> Error in listFilters(mart, what = "type") :
> The function argument 'what' contains an invalid value: type
> Valid are: name, description, options, fullDescription
>
> I also tried out with listFilters function :
> listFilters("chromosome_name",mart=mart), which results in the same error.
>
> What is going on here, and how can I rectify it ?
>
> Here is my session info:
>
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] GenomeGraphs_1.0.1 biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.6-0
>
>
> Thanks,
> Tejal
>
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>
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