Description Usage Arguments Details Value Author(s) References Examples
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'.
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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. |
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 a table closely corresponding to the web interface output.
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
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