download.kegg: Download KEGG pathway graphs and associated KGML data

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

This is the downloader function for KEGG pathways, automatically download graph images and associated KGML data.

Usage

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download.kegg(pathway.id = "00010", species = "hsa", kegg.dir = ".",
file.type=c("xml", "png"))

Arguments

pathway.id

character, 5-digit KEGG pathway IDs. Default pathway.id="00010".

species

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.

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.

Value

a named character vector, either "succeed" or "failed", indicating the download status of corresponding pathways.

Author(s)

Weijun Luo <[email protected]>

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

pathview the main function, node.info the parser,

Examples

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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

BowenNCSU/pathview documentation built on May 24, 2019, 7:36 a.m.