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

Paolo Martini paolo.martini at unipd.it
Wed Mar 18 11:00:54 CET 2015

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"

> 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

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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

Paolo Martini
c/o Lab Romualdi
via U. Bassi 58/b
35121 Padova, Italy
Tel: 049 8276319
Fax: 049 8276159
e-mail: paolo.martini at unipd.it

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