makeGeneNetwork: Expand reactions / complexes into their gene constituents.

In ahmohamed/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Expand reactions / complexes into their gene constituents.

Description

These are general functions to expand vertices by their attributes, i.e. create a separate vertex for each attribute value.

Usage

expandComplexes(
  graph,
  v.attr,
  keep.parent.attr = "^pathway",
  expansion.method = c("normal", "duplicate"),
  missing.method = c("keep", "remove", "reconnect")
)

makeGeneNetwork(
  graph,
  v.attr = "genes",
  keep.parent.attr = "^pathway",
  expansion.method = "duplicate",
  missing.method = "remove"
)

Arguments

graph	An annotated igraph object.
v.attr	Name of the attribute which vertices are expanded to.
keep.parent.attr	A (List of) regex experssions representing attributes to be inherited by daughter vertices. If "all" is passed, all parent attributes are inherited.
expansion.method	If "duplicate", attribute values sharing more than one parent vertex are duplicated for each vertex they participate in. For exmaple, if one gene G1 catalyzes reactions R1, R2; then G1##R1, and G1##R2 vertices are created. If "normal" only one vertex (G1) is created, and inherit all R1 and R2 connections and attributes.
missing.method	How to deal with vertices with no attribute values. "keep" retains the parent node, "remove" simply deletes the vertex, and "reconnect" removes the vertex and connect its neighbours to each other (to prevent graph cuts).

Details

These 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 expand metabolite vertices by "miriam.kegg.compound" attribute.

Value

A new graph with vertices expanded.

makeGeneNetwork returns a graph, where nodes are genes, and edges represent participation in succesive reactions.

Author(s)

Ahmed Mohamed

See Also

Other Network processing methods: makeMetaboliteNetwork(), makeReactionNetwork(), reindexNetwork(), 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)

ahmohamed/NetPathMiner documentation built on Oct. 31, 2024, 8:01 a.m.