gProfileR (version 0.7.0)

gconvert: 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.

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")
# }