ToPASeq (version 1.6.0)

reduceGraph: Function to reduce the pathway graph

Description

Function simplifies a pathway graph topology. It merges a user specified nodes into a one. The specified set of nodes must be either a gene family or a protein complex. By a gene family we mean a set of genes with same outgoing or incoming edges. On the other hand, a protein complex is a set of nodes with only undirected binding edges between them and the number of edges is equal to the complex size.

Usage

reduceGraph(graph, reduction)

Arguments

graph

An object of class Pathway, a pathway to be reduced

reduction

A named list of reductions to be maded.

Value

A Pathway

Examples

pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")


#gr<-as(pathways,"pathway")
red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("SHC1", "SHC4","SHC2","SHC3"))
reduced<-reduceGraph(pathways, red)
reduced
par(mfrow=c(1,2))

nA<-list(fillcolor=c(NRAS="red", KRAS="red", HRAS="red", SHC1="green", SHC4="green", SHC2="green", SHC3="green"))
plot(as(pathways,"graphNEL"), nodeAttrs=nA, attrs=list(node=list(fontsize=30, height=40)), main="Before")

plot(as(reduced,"graphNEL"), 
 nodeAttrs=list(fillcolor=c(RAS="red", SHC="green")), attrs=list(node=list(fontsize=30, height=40)), main="After")

#this throws an error, "RELA", "FOS","NFKB1" is not correct set of genes
## Not run: 
# pathways<-pathways("hsapiens","kegg")["Prolactin signaling pathway"]
# pathways<-convertIdentifiers(pathways[[1]], "SYMBOL")
# 
# 
# gr<-convertIdentifiers(kegg[["Prolactin signaling pathway"]],"SYMBOL")
# red<-list(RAS=c("NRAS","KRAS","HRAS"), SHC=c("RELA", "FOS","NFKB1"))
# reduced<-reduceGraph(pathways, red)
# ## End(Not run)