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

[Stefan McKinnon Edwards]

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
$SERPINA1
[1] "NM_173882" "NP_776307"

$KERA
[1] "NM_173910" "NP_776335"

$CD5
[1] "NM_173899" "NP_776324"

R> pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')
$SERPINA1
[1] "NP_776307"

$KERA
[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