getComponents {gene2pathway} | R Documentation |
1. get connected pathway components; 2. get all elements of a given pathway; 3. color certain elements in a pathway.
getComponents(pathway.id) get.elements.by.pathway(pathway.id) color.pathway.by.elements(pathway.id, elements)
pathway.id |
KEGG pathway ID, e.g. "path:hsa04012" |
elements |
KEGG element IDs: character vector of numbers |
All functions use the KEGG SOAP service.
getComponents: a list with the entries
geneIDs |
Entrez gene IDs mapping to each pathway component |
elemIDs |
KEGG element IDs mapping to each pathway component |
get.elements.by.pathway: list, see <URL http://www.genome.jp/kegg/soap/doc/keggapi_manual.html> for details
color.pathway.by.elements: an URL of a colored gif file, see <URL http://www.genome.jp/kegg/soap/doc/keggapi_manual.html> for details
Holger Froehlich
## Not run: comp = getComponents("path:hsa04020") # get all connected components color.pathway.by.elements("path:hsa04020", comp$elemIDs[[1]]) # mark first component ## End(Not run)