getOrthologs {bioCancer} | R Documentation

## Performs quicker lookup for orthologs in homologe data packages

### Description

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.

### Usage

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

### 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`.

### 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

    tmp <-1

[Package bioCancer version 1.22.0 Index]