gconvert: Convert gene IDs.

In gProfileR: Interface to the 'g:Profiler' Toolkit

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 <[e-mail]>, Raivo Kolde <[e-mail]>, Tambet Arak <[e-mail]>

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)

gProfileR documentation built on Nov. 6, 2019, 5:08 p.m.