[Bioc-devel] New package with methods for annotation packages

Vincent Carey stvjc at channing.harvard.edu
Fri Jan 7 16:14:16 CET 2011

My sense is that the task can be accomplished using GSEABase where
your symbol vector needs to be a GeneSet instance with a specified
semantics for the geneIds in a given slot.  One then changes the
annotation semantics with specific methods and the token set is
translated.  This is not to say that there is an important redundancy
between your interface and GSEABase -- I can't form an opinion yet.
However I think it would be good to reuse the GSEABase infrastructure
for the task -- noting functionality gaps if some are found -- and to
encourage users to think about programming with gene sets in a more
semantically rich context than that provided by vectors of strings.

On Fri, Jan 7, 2011 at 8:46 AM, Stefan McKinnon Edwards
<StefanM.Edwards at agrsci.dk> wrote:
> Hi all,
> I have compiled a package of methods to ease the use of the annotation data packages from the Biocore Data Team (such as "org.Bt.eg.db"). It basically provides a routine for mapping biological entities from one identifier (e.g. Ensembl) to another (e.g. RefSeq) by the use of the aforementioned data packages. In the case with org.Bt.eg.db, one would have to map from Ensembl to Entrez and then to RefSeq, and meanwhile cleaning the result. With my package, it can be done with a single line. Here is an example:
> R> library(AnnotationFuncs)
> R> library(org.Bt.eg.db)
> R> symbols <- c("SERPINA1","KERA","CD5")
> R> refseq <- translate(symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
> R> refseq
> [1] "NM_173882" "NP_776307"
> [1] "NM_173910" "NP_776335"
> $CD5
> [1] "NM_173899" "NP_776324"
> R> pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')
> [1] "NP_776307"
> [1] "NP_776335"
> # End of example.
> For this, I have two questions:
> 1) Is there any other package on CRAN or BioConductor that provides the same functionality?
> 2) I was thinking of making a small Application Note to e.g. Oxford Journals Bioinformatics. Would there be any issue, if I already have posted the package on my personal website?
> Kind regards,
> Stefan McKinnon Edwards
> PhD student
> Dept. of Genetics and Biotechnology
> Faculty of Agricultural Sciences
> Aarhus University
> Blichers Allé 20, Postboks 50
> DK-8830 Tjele
> Tel.: +45 8999 1291
> Email: stefanm.edwards at agrsci.dk
> Tel.: +45 8999 1900
> Web: www.agrsci.au.dk
> _______________________________________________
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