gorth: Find orthologs.
In raivokolde/gProfileR: g:ProfileR

Description Usage Arguments Details Value Author(s) References Examples

Interface to the g:Orth web toolkit. Organism names are constructed by combining the first letter of the name and family name. For example human - 'hsapiens' and mouse - 'mmusculus'.

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  gorth(genelist, source_organism = "hsapiens",
    target_organism = "mmusculus", region_query = F,
    numeric_ns = "", mthreshold = 3, df = T)

`genelist`	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`	how many ortholog names per gene to show.
`df`	logical indicating whether the output will be a data.frame or list.

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.

The output can be either a list or a data.frame. The list has an entry for every input gene. The data frame is just a two column table with inputs and corrsponding outputs. The input names may be duplicated.

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

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