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