download.kegg.pathways {EnrichmentBrowser} | R Documentation |
The function downloads all metabolic and non-metabolic pathways in KEGG XML format for a specified organism.
download.kegg.pathways( org, cache=TRUE, out.dir = NULL, zip = FALSE )
org |
Organism in KEGG three letter code, e.g. ‘hsa’ for ‘homo sapiens’. |
cache |
Logical.
Should a locally cached version used if available?
Defaults to |
out.dir |
Output directory. If not null, pathways are written to files in the specified directory. |
zip |
Logical. In case pathways are written to file (‘out.dir’ is not null): should output files be zipped? |
if(is.null(out.dir)): a list of KEGGPathway objects else: none, as pathways are written to file
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
keggList
, keggGet
,
KEGGPathway-class
,
parseKGML
pwys <- download.kegg.pathways("hsa")