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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
