gProfileR (version 0.2)

gconvert: Convert gene IDs.

Description

Convert gene IDs.

Usage

gconvert(query, organism="hsapiens", target="ENSG", region_query=F,
    numeric_ns="", 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.

df

logical indicating whether the output will be a data.frame or list.

Value

• The output can be either list or data.frame. List has an entry for every input gene. Data frame is just a two column table with inputs and corrsponding outputs. The input names may be duplicated.

Details

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'.

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

gconvert(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")

# Get all mouse Cell cycle genes 
gconvert(c("GO:0007049"), organism = "mmusculus")