gorth: Find orthologs.

In gProfileR: Interface to the 'g:Profiler' Toolkit

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 <[e-mail]>, Juri Reimand <[e-mail]>, Tambet Arak <[e-mail]>

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

## Not run: 
 gorth(c("Klf4","Pax5","Sox2","Nanog"), source_organism="mmusculus", target_organism="hsapiens")

## End(Not run)

gProfileR documentation built on Nov. 6, 2019, 5:08 p.m.