getComponents {gene2pathway}R Documentation

KEGG pathway information

Description

1. get connected pathway components; 2. get all elements of a given pathway; 3. color certain elements in a pathway.

Usage

getComponents(pathway.id)

get.elements.by.pathway(pathway.id)

color.pathway.by.elements(pathway.id, elements)

Arguments

pathway.id KEGG pathway ID, e.g. "path:hsa04012"
elements KEGG element IDs: character vector of numbers

Details

All functions use the KEGG SOAP service.

Value

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

Author(s)

Holger Froehlich

Examples

## 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)

[Package gene2pathway version 1.2.0 Index]