reindexNetwork {NetPathMiner} | R Documentation

## Replaces current vertex ids with chosen attribute.

### Description

This function allows users to replace vertex ids with another attribute, calculating connectivities based on the new attribute.

### Usage

    reindexNetwork(graph, v.attr)

### Arguments

`graph` | An annotated igraph object.
`v.attr` | Name of the attribute to use as vertex ids.

### Details

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.

### Value

A new graph with vertices expanded.

### Author(s)

Ahmed Mohamed

### See Also

Other Network processing methods: `expandComplexes`, `makeMetaboliteNetwork`, `makeReactionNetwork`, `rmSmallCompounds`, `simplifyReactionNetwork`, `vertexDeleteReconnect`

### Examples

     ## 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)

[Package NetPathMiner version 1.28.0 Index]