Annotation translation functions

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Description

Package: AnnotationFuncs
Type: Package
Version: 1.3.0
Date: 2011-06-10
License: GPL-2
LazyLoad: yes

Details

Functions for handling translations between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db). Primary functions are translate for translating and getOrthologs for efficient lookup of homologes using the Inparanoid databases. Other functions include functions for selecting Refseqs or Gene Ontologies (GO).

Author(s)

Stefan McKinnon Edwards stefan.hoj-edwards@agrsci.dk

References

http://www.iysik.com/index.php?page=annotation-functions

See Also

translate, getOrthologs

Examples

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library(org.Bt.eg.db)
gene.symbols <- c('DRBP1','SERPINA1','FAKE','BLABLA')
# Find entrez identifiers of these genes.
eg <- translate(gene.symbols, org.Bt.egSYMBOL2EG)
# Note that not all symbols were translated.

# Go directly to Refseq identifiers.
refseq <- translate(gene.symbols, from=org.Bt.egSYMBOL2EG, to=org.Bt.egREFSEQ)
# Pick the proteins:
pickRefSeq(refseq, priorities=c('NP','XP'), reduce='all')