[BioC] getBM function in biomaRt

[Steffen at stat.Berkeley.EDU]

Hi Tim,

biomaRt works with archives from about Ensembl version 52 and upwards.
Hg17 corresponds to NCBI35 which is in Ensembl 35, you'll need to get a
very old archive.
You could get the data you need via the web BioMart interface:

http://nov2005.archive.ensembl.org/index.html

follow the BioMart link to make a query.

Hope this helps,
Steffen

> Hi,
>
> I wanted to get some exon information for specific genes. I wanted to use
> the hg17 build, since my SNP data is based on that. The code that I use
> is:
> -------------------------------------
> library(biomaRt)
>  entrezid <- "8334"
>  martx <- "ensembl_mart_49"
>
>  ensembl <- useMart(biomart=martx,dataset="hsapiens_gene_ensembl",
>                     archive=TRUE)     ### "ensembl_mart_49" hg17 for wtccc
>     zz <- getBM(attr = c("entrezgene","exon_stable_id",
>                 "exon_chrom_start","exon_chrom_end"),
>                 filters="with_entrezgene",
>                  values = entrezid,mart = ensembl)
>
>
> ------------------------------------
> However, I get the following error:
> Error in listFilters(mart, what = "type") :
>   The function argument 'what' contains an invalid value: type
> Valid are: name, description, options, fullDescription, filters5, filters6
>
> I checked with listFilters(ensembl) and ?getBM, and the filters appear to
> be ok. What am I doing wrong?
> thanks!
> My sessionInfo():
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> [7] base
>
> other attached packages:
>  [1] GOstats_2.12.0      graph_1.24.1        Category_2.12.0
>  [4] GO.db_2.3.5         multtest_2.2.0      XML_2.6-0
>  [7] hgu133a.db_2.3.5    org.Hs.eg.db_2.3.6  RSQLite_0.7-3
> [10] AnnotationDbi_1.8.0 GEOquery_2.8.0      RCurl_1.2-1
> [13] bitops_1.0-4.1      biomaRt_2.2.0       DBI_0.2-4
> [16] RColorBrewer_1.0-2  genefilter_1.28.0   affy_1.24.1
> [19] Biobase_2.6.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.14.0        annotate_1.24.0
>  [3] GSEABase_1.8.0       MASS_7.3-3
>  [5] preprocessCore_1.8.0 RBGL_1.20.0
>  [7] splines_2.10.0       survival_2.35-7
>  [9] tools_2.10.0         xtable_1.5-6
>>
>
>
>
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>
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