getOrthologs: Performs quicker lookup for orthologs in homologe data...
In AnnotationFuncs: Annotation translation functions

Description Usage Arguments Details Value Author(s) References See Also Examples

Performs quicker lookup for orthologs in homologe data packages

1 2	getOrthologs(values, mapping, genus, threshold=1, pre.from, pre.to, post.from, post.to, ...)

`values`	Vector, coerced to character vector, of values needed mapping by homology.
`mapping`	Homology mapping object, such as `hom.Hs.inpBOSTA` or `revmap(hom.Hs.inpBOSTA)`.
`genus`	Character vector. 5 character INPARANOID style genus name of the mapping object, e.g. 'BOSTA' for both `hom.Hs.inpBOSTA` and `revmap(hom.Hs.inpBOSTA)`.
`threshold`	Numeric value between 0 and 1. Only clustered homologues with a parwise score above the threshold is included. The native implementation has this set to 1.
`pre.from`	Mapping object if `values` needs translation before mapping. E.g. `values` are entrez and `hom.Hs.inpBOSTA` requires ENSEMBLPROT, `hom.Hs.inpAPIME` requires Refseq (?). Arguments `from` and `to` are just like in `translate`.
`pre.to`	Second part of translation before mapping.
`post.from`	Translate the result from homology mapping to a desired id; just like in `translate`.
`post.to`	Second part of translation after mapping.
`...`	Additional arguments sent to `translate`.

Using the INPARANOID data packages such as hom.Hs.inp.db is very, very slow and can take up to 11 min (on this particular developers workstation). This function introduces a new method that can do it in just 20 seconds (on the developers workstation). In addition, it includes options for translating between different identifers both before and after the mapping.

List. Names of list corresponds to values, except those that could not be mapped nor translated. Entries are character vectors.

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

?hom.Hs.inp.db - http://inparanoid.sbc.su.se/

Berglund, A.C., Sjolund, E., Ostlund, G., Sonnhammer, E.L.L. (2008) InParanoid 6: eukaryotic ortholog clusters with inparalogs Nucleic Acids Res. 36:D263–266

O'Brien, K.P., Maido, R., Sonnhammer, E.L.L (2005) Inparanoid: A Comprehensive Database of Eukaryotic Orthologs NAR 33:D476–D480

Remm, M., Storm, C.E.V, Sonnhammer, E.L.L (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol. 314:1041–1052

translate, .getTableName, mapLists

library(hom.Hs.inp.db)
library(org.Hs.eg.db)
library(org.Bt.eg.db)
getOrthologs("ENSBTAP00000024572", revmap(hom.Hs.inpBOSTA), 'BOSTA') 
# And now, we will map from entrez genes 1, 2 and 3 to bovine Refseq
bovine.ensembl <- getOrthologs(c(1,2,3), hom.Hs.inpBOSTA, 'BOSTA', pre.from=org.Hs.egENSEMBLPROT, post.from=org.Bt.egENSEMBLPROT2EG)
refseqs <- translate(unlist(bovine.ensembl, use.names=FALSE), org.Bt.egREFSEQ)
hs2bt.refseqs <- mapLists(bovine.ensembl, refseqs)
# Another way of doing it:
hs2bt.refseqs2 <- lapply(bovine.ensembl, translate, from=org.Bt.egREFSEQ, simplify=TRUE) # simplify=TRUE is very important here!