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

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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

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