[BioC] getBM and sqldf error - no such table

[James W. MacDonald]

Hi David,

The error has to do with sqldf, which is a CRAN package, rather than 
biomaRt. Because of that, you should be asking this question on R-help 
(r-help at r-project.org) rather than this listserv.

Best,

Jim


On 5/6/2014 5:17 AM, David [guest] wrote:
> Hello,
>
> I retrieved some attributes from the ensembl database using biomaRt, but I get an error when trying to perform sql commands with sqldf.
>
> My code:
> ****
> library(biomaRt)
> library(sqldf)
>
> mart <- useMart("ensembl")
> ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
>
> gene.data <- getBM(attributes=c('go_id','hgnc_symbol', 'ensembl_transcript_id'),
>                                 filters = 'go_id', values = "GO:0001771", mart = ensembl)
>
> gene.data_s <- sqldf("select distinct * from gene.data order by go_id, hgnc_symbol")
> ****
>
> output:
>
>> Error in sqliteExecStatement(con, statement, bind.data) :
>>     RS-DBI driver: (error in statement: no such table: gene.data)
>
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  tcltk     stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] BiocInstaller_1.12.1  stringr_0.6.2         data.table_1.9.2      biomaRt_2.18.0
>   [5] GO.db_2.10.1          AnnotationDbi_1.24.0  Biobase_2.22.0        BiocGenerics_0.8.0
>   [9] sqldf_0.4-7.1         RSQLite.extfuns_0.0.1 RSQLite_0.11.4        DBI_0.2-7
> [13] gsubfn_0.6-5          proto_0.3-10
>
> loaded via a namespace (and not attached):
> [1] chron_2.3-45   IRanges_1.20.7 plyr_1.8.1     Rcpp_0.11.1    RCurl_1.95-4.1 reshape2_1.4   stats4_3.0.2
> [8] tools_3.0.2    XML_3.95-0.2
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099