Mapping species name to KEGG code

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Description

This function maps species name to KEGG code.

Usage

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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

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