kegg.species.code {pathview} | R Documentation

## Mapping species name to KEGG code

### Description

This function maps species name to KEGG code.

### Usage

    kegg.species.code(species = "hsa", na.rm = FALSE, code.only = TRUE)

### Arguments

`species` | character, either the KEGG code, scientific name or the common name of the target species. Default species="hsa", it is equivalent to use either "Homo sapiens" (scientific name) or "human" (common name).
`na.rm` | logical, should unmapped entris be removed. Default na.rm = FALSE.
`code.only` | logical, whether to extract KEGG species code only or with gene ID usage info too. Default , code.only = TRUE.

### Value

a character vector of mapped KEGG code of species.

### Author(s)

Weijun Luo <luo_weijun@yahoo.com>

### References

Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285

### See Also

`korg` the species and KEGG code mapping data, `cpd2kegg` etc the auxillary compound ID mappers, `download.kegg` the downloader function.

### Examples

    species=c("ptr", "Mus musculus", "dog", "happ")
    kcode=kegg.species.code(species = species, na.rm = FALSE)
    print(kcode)

[Package pathview version 1.20.0 Index]