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

[Marc Carlson]

Ok I spoke a little too quickly earlier.  Looking back, there should
indeed be a field from columns() called 'ORF' and it is basically used
here as the central gene ID for this single package.  But the code for
keys (and columns) was getting this 'ORF' conflated with the other 'ORF'
used in resources from SGD (which this has nothing to do with since the
data all comes from plasmoDB).

Anyhow, I have fixed the software bugs and pushed a patch to release and
devel.  It should be up in about a day.

   Marc



On 03/18/2015 10:23 AM, Marc Carlson wrote:
> 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
>>
>>
>
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