character, either the KEGG code, scientific name or the common name of
the target species. When KEGG ortholog pathway is considered,
species="ko". Default species="hsa", it is equivalent to use either
"Homo sapiens" (scientific name) or "human" (common name).
kegg.dir
character, the directory of KEGG pathway data file (.xml) and image file
(.png). Default kegg.dir="." (current working directory).
file.type
character, the file type(s) to be downloaded, either KEGG pathway data
file (xml) or image file (png). Default include both types.
Value
a named character vector, either "succeed" or "failed", indicating the
download status of corresponding pathways.
Details
Species can be specified as either kegg code, scientific name or the
common name. Scientific name and the common name are always mapped to
kegg code first.
Length of species should be either 1 or the same as pathway.id, if
not, the same set of pathway.id will be applied to all species.
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
data(demo.paths)
sel.2paths=demo.paths$sel.paths[1:2]
download.kegg(pathway.id = sel.2paths, species = "hsa")
#pathway files should be downloaded into current working directory