getOrthologs: Performs quicker lookup for orthologs in homologe data...

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

Description

Performs quicker lookup for orthologs in homologe data packages

Usage

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

Arguments

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.

Details

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.

Value

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

Author(s)

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

References

?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

See Also

translate, .getTableName, mapLists

Examples

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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!


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