gconvert {gProfileR} | R Documentation |
Convert gene IDs.
Description
Interface to the g:Convert tool. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'.
Usage
gconvert(query, organism = "hsapiens", target = "ENSG",
region_query = F, numeric_ns = "", mthreshold = Inf,
filter_na = T, df = T)
Arguments
query |
list of gene IDs. |
organism |
organism name. |
target |
target namespace. |
region_query |
interpret query as chromosomal ranges. |
numeric_ns |
namespace to use for fully numeric IDs. |
mthreshold |
maximum number of results per initial alias to show. |
filter_na |
logical indicating whether to filter out results without a corresponding target. |
df |
logical indicating whether the output will be a data.frame or list. |
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)
Juri Reimand <jyri.reimand@ut.ee>, Raivo Kolde <rkolde@gmail.com>, 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:
gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")
## End(Not run)