Description Objects from the Class Slots Methods Author(s) References Examples
A class to present 'reaction' elements in KGML files
Objects can be created by calls of the function parseReaction
.
name
:Object of class "character"
the KEGGID of
this reaction, e.g. "rn:R02749"
type
:Object of class "character"
the type of
this reaction, either 'reversible' or 'irreversible'
substrateName
:Object of class "character"
,
KEGG identifier of the COMPOUND database or the GLYCAN database
e.g. "cpd:C05378"
substrateAltName
:Object of class "character"
alternative name of its parent substrate element
productName
:Object of class "character"
specifies the KEGGID of the product
productAltName
:Object of class "character"
alternative name of its parent product element
signature(object = "KEGGReaction")
: show method
signature(object = "KEGGReaction")
: get the
KEGGID of the reaction
signature(object = "KEGGReaction")
: get the
type of the reaction
signature(object = "KEGGReaction")
: get the
name of substrate
signature(object = "KEGGReaction")
: get the
name of product
Jitao David Zhang mailto:jitao_david.zhang@roche.com
KGML Document Manual http://www.genome.jp/kegg/docs/xml/
1 2 3 4 5 6 7 8 9 10 11 12 | ## We show how to extract reactions from a 'KEGGPathway' object
mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
maptest <- parseKGML(mapfile)
mapReactions <- getReactions(maptest)
## More details about reaction
reaction <- mapReactions[[1]]
getName(reaction)
getType(reaction)
getSubstrate(reaction)
getProduct(reaction)
|
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