reindexNetwork {NetPathMiner} | R Documentation |
This function allows users to replace vertex ids with another attribute, calculating connectivities based on the new attribute.
reindexNetwork(graph, v.attr)
graph |
An annotated igraph object. |
v.attr |
Name of the attribute to use as vertex ids. |
This functions can be very useful when merging networks constructed from different databases. For example, to match a network created from Reactome to a KEGG network, you can reindex the vertices by "miriam.kegg.compound" attribute. Another usage is to remove duplicated vertices (in case of different subcellular compartments, for example). if a network has ATP_membrane & ATP_cytoplasm vertices, reindexing by chemical name will collapse them into one 'ATP' vertex.
A new graph with vertices expanded.
Ahmed Mohamed
Other Network processing methods: expandComplexes
,
makeMetaboliteNetwork
,
makeReactionNetwork
,
rmSmallCompounds
,
simplifyReactionNetwork
,
vertexDeleteReconnect
## Make a gene network from a reaction network. data(ex_sbml) # A bipartite metbaolic network. rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE) ggraph <- makeGeneNetwork(rgraph) ## Expand vertices into their contituent genes. data(ex_kgml_sig) # Ras and chemokine signaling pathways in human ggraph <- expandComplexes(ex_kgml_sig, v.attr = "miriam.ncbigene", keep.parent.attr= c("^pathway", "^compartment")) ## Create a separate vertex for each compartment. This is useful in duplicating ## metabolite vertices in a network. ## Not run: graph <- expandComplexes(graph, v.attr = "compartment", keep.parent.attr = "all", expansion.method = "duplicate", missing.method = "keep") ## End(Not run)