| subKEGGgraph {KEGGgraph} | R Documentation |
subKEGGgraph extends generic method subGraph and subsets the KEGG
graph. Both 'subKEGGgraph' and 'subGraph' can be used to subset the
graph, the difference lies in whether the node and edge attributes
from KEGG are also subset (subKEGGgraph) or not
(subGraph).
See details below.
subKEGGgraph(nodes, graph)
nodes |
Node names to subset |
graph |
A graph parsed from KGML files, produced by
parseKGML2Graph, KEGGpathway2Graph or parseKGMLexpandMaps |
subGraph does not subset the
node or edge attributes, hence the results of
getKEGGnodeData and getKEGGedgeData does
not map to the nodes and edges in the subgraph in a one-to-one
manner, with attributes of removed nodes and edges still remaining in
the subGraph.
subKEGGgraph calls subGraph first to subset the graph,
and then it also subsets the KEGGnodeData and KEGGedgeData so that
they are one-to-one mapped to the nodes and edges in the subgraph.
A graph with nodeData and edgeData.
Jitao David Zhang mailto:j.zhang@dkfz.de
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
subs <- c("hsa:1432",edges(gR)$`hsa:1432`,"hsa:5778","hsa:5801",
"hsa:84867","hsa:11072","hsa:5606","hsa:5608","hsa:5494","hsa:5609")
gR.keggsub <- subKEGGgraph(subs, gR)
gR
gR.keggsub