nem (version 2.46.0)

SCCgraph: Combines Strongly Connected Components into single nodes

Description

SCCgraph is used to identify all nodes which are not distinguishable given the data.

Usage

SCCgraph(x,name=TRUE,nlength=20)

Arguments

x

graphNEL object or an adjacency matrix

name

Concatenate all names of summarized nodes, if TRUE, or number nodes, if FALSE. Default: TRUE

nlength

maximum length of names

Value

graph

a graphNEL object with connected components of the input graph summarized into single nodes

scc

a list mapping SCCs to nodes

which.scc

a vector mapping nodes to SCCs

Details

A graph inferred by either nem or nemModelSelection may have cycles if some phenotypic profiles are not distinguishable. The function SCCgraph identifies cycles in the graph (the strongly conneced components) and summarizes them in a single node. The resulting graph is then acyclic.

See Also

nem, transitive.reduction

Examples

   data("BoutrosRNAi2002")
   D   <- BoutrosRNAiDiscrete[,9:16]
   res <- nem(D,control=set.default.parameters(unique(colnames(D)), para=c(.13,.05)))
   # 
   sccg <- SCCgraph(res$graph,name=TRUE)
   #
   par(mfrow=c(1,2))
   if(require(Rgraphviz)){
    plot.nem(res, main="inferred from data")      
    plot(sccg$graph, main="condensed (rel,key)")
    }