[BioC] getBM and sqldf error - no such table

[David [guest]]

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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