R: Convert gene IDs.

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

    gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")

[Package gProfileR version 0.6.1 Index]