getDisplayName-methods: Get a character string as label for display
In Accio/KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
getDisplayName-methods R Documentation
Get a character string as label for display
Description
In KGML files, 'graph' element has a 'name' attribute to store the
displaying name of a node, which is straighforward for end users. For
example, biologists have no idea about a node 'hsa:1432' but its
display name 'MAPK14' helps them to link this node to their knowledge.
This method extract DisplayName from graph objects for KEGGNode and graph, where the
method for graph returns the display names of its nodes.
Methods
- object = "KEGGNode"
An object of KEGGNode-class
- object = "graph"
A KEGG graph object
Author(s)
Jitao David Zhang mailto:jitao_david.zhang@roche.com
References
KGML Document Manual https://www.genome.jp/kegg/docs/xml/
Examples
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
pathway <- parseKGML(sfile)
nodes <- nodes(pathway)
subnodes <- nodes[10:15]
sapply(subnodes, getDisplayName)
## compare them with getName, one 'displayName' may correspond to many paralogues
sapply(subnodes, getName)
Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.
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| getDisplayName-methods | R Documentation |
Get a character string as label for display
Description
In KGML files, 'graph' element has a 'name' attribute to store the displaying name of a node, which is straighforward for end users. For example, biologists have no idea about a node 'hsa:1432' but its display name 'MAPK14' helps them to link this node to their knowledge. This method extract DisplayName from graph objects for KEGGNode and graph, where the method for graph returns the display names of its nodes.
Methods
- object = "KEGGNode"
An object of
KEGGNode-class- object = "graph"
A KEGG graph object
Author(s)
Jitao David Zhang mailto:jitao_david.zhang@roche.com
References
KGML Document Manual https://www.genome.jp/kegg/docs/xml/
Examples
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
pathway <- parseKGML(sfile)
nodes <- nodes(pathway)
subnodes <- nodes[10:15]
sapply(subnodes, getDisplayName)
## compare them with getName, one 'displayName' may correspond to many paralogues
sapply(subnodes, getName)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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