[Bioc-devel] keys function of org.Pf.plasmo.db gives an error.

[Marc Carlson]

Hi Paolo,

The ORF type has never been available for that package.  This is a bug 
in the columns method (which I will now fix).  Thanks for reporting it.

  Marc



On 03/18/2015 03:00 AM, Paolo Martini wrote:
> Dear Bioconductor,
>
> I am working with the annotation package "org.Pf.plasmo.db".
>
> I tried to get the keys from the "ORF" column.
>
>> library(org.Pf.plasmo.db)
>> columns(org.Pf.plasmo.db)
>   [1] "ORF"         "ENZYME"      "PATH"        "SYMBOL"      "GENENAME"
>   [6] "GO"          "EVIDENCE"    "ONTOLOGY"    "GOALL"       "EVIDENCEALL"
> [11] "ONTOLOGYALL" "ALIAS2ORF"
>
>> keys(org.Pf.plasmo.db, "ORF")
> Error in sqliteSendQuery(con, statement, bind.data) :
>    error in statement: no such table: sgd
>
>
> I tried both stable and devel version but neither the stable nor the devel
> seemed to work.
>
> To my knowledge sgd is related to S. cerevisiae.
>
> Is the "ORF" keytype availble for Malaria?
>
> Thanks a lot.
>
>> sessionInfo()
> R Under development (unstable) (2015-03-16 r67994)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> Running under: Ubuntu 14.10
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] org.Pf.plasmo.db_3.1.0 RSQLite_1.0.0          DBI_0.3.1
> [4] AnnotationDbi_1.29.17  GenomeInfoDb_1.3.13    IRanges_2.1.43
> [7] S4Vectors_0.5.22       Biobase_2.27.2         BiocGenerics_0.13.6
>
>