gconvert: Convert gene IDs.

In raivokolde/gProfileR: g:ProfileR

Description

Interface to the g:Convert web toolkit.

Usage

  gconvert(ids, organism = "hsapiens", target = "ENSG",
    region_query = F, numeric_ns = "", df = T)

Arguments

ids	a vector of gene IDs.
organism	gene list origin.
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.

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

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

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

raivokolde/gProfileR documentation built on May 26, 2019, 9:57 p.m.