rewSim | R Documentation |
This function performs the rewiring simulation for the input
rewSim(g,nDup,dDup,rewProb,methods=c(),nRep = 1,nThreads =1) ## S3 method for class 'CoReg.rewSim' print(CoReg.rewSim) ## S3 method for class 'CoReg.rewSim' summary(CoReg.rewSim) ## S3 method for class 'CoReg.rewSim' plot(CoReg.rewSim)
g |
The input transcription network. This should be an "igraph" object returned by the function |
nDup |
Numeric value specifying number of the genes to be duplicated. These duplicated genes will be rewired |
dDup |
Numeric value specifying the minimum degree for the genes to be duplicated. This function first ranks the genes based on their degrees. Then randomly selected |
rewProb |
A vector specifying the a series of rewiring probabilities |
methods |
Clustering methods to be compared with CoReg. Available options are: "coregJac" (CoReg + Jaccard index), "coregGeo" (CoReg + geometric index),"coregInv" (CoReg + inverse log-weighted index),"lp" (label propagation),"wt" (walk trap),"eb" (edge betweenness) |
nRep |
Number of replicates for run of rewiring simulation |
nThreads |
Number of threads for running the simulation. Only valid when "coregGeo" is selected in |
CoReg.rewSim |
|
This function performs the rewiring simulation for the network. The simulation starts with duplicating nDup
genes with degrees greater than dDup
. Then the duplicated genes will be rewired using a series of rewiring probability specified by rewProb
. The result can be plotted using generic function plot()
An object of class CoReg.rewSim
Qi Song
Qi S., Ruth G., Lenwood SH. Song L. (2017). Identification of regulatory modules in genome scale transcription regulatory networks. BMC Systems Biology. 2017 11:140.
CoReg
data(athNet, package="CoReg") simRe<-rewSim(athNet,nDup = 50, dDup = 10, c(0.3,0.5),c("coregJac","lp","wt","eb"),2) # Display simulation result print(simRe) simRe$evalResult # Plot simulation result plot(simRe)
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