R: Find orthologs.

gorth {gProfileR} | R Documentation

## Find orthologs.

### Description

Interface to the g:Orth tool. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.

### Usage

    gorth(query, source_organism = "hsapiens", target_organism = "mmusculus",
      region_query = F, numeric_ns = "", mthreshold = Inf, filter_na = T,
      df = T)

### Arguments

`query` | list of gene IDs to be translated.
`source_organism` | name of the source organism.
`target_organism` | name of the target organism.
`region_query` | interpret query as chromosomal ranges.
`numeric_ns` | namespace to use for fully numeric IDs.
`mthreshold` | maximum number of ortholog names per gene to show.
`filter_na` | logical indicating whether to filter out results without a corresponding target name.
`df` | logical indicating whether the output will be a data.frame or list.

### Details

To alleviate the problem of having many orthologs per gene (most of them uninformative) one can set a threshold for the number of results. The program tries to find the most informative by selecting the most popular ones.

### Value

The output can be either a list or a data.frame. The list has an entry for every input gene. The data frame is a table closely corresponding to the web interface output.

### Author(s)

Raivo Kolde <rkolde@gmail.com>, Juri Reimand <juri.reimand@ut.ee>, Tambet Arak <tambet.arak@gmail.com>

### References

J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler – a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200

### Examples

    gorth(c("Klf4","Pax5","Sox2","Nanog"), source_organism="mmusculus", target_organism="hsapiens")

[Package gProfileR version 0.6.1 Index]