rewSim: Rewiring simulation for the network

View source: R/simulation.R

rewSimR Documentation

Rewiring simulation for the network

Description

This function performs the rewiring simulation for the input

Usage

  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)

Arguments

g

The input transcription network. This should be an "igraph" object returned by the function "loadNetwork"

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 nDup genes of which the degrees are greater than dDup. If number of genes above the threshold is smaller than nDup, all the genes above the threshold will be 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 Methods

CoReg.rewSim

CoReg.rewSim object

Details

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()

Value

An object of class CoReg.rewSim

Author(s)

Qi Song

References

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.

See Also

CoReg

Examples

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)


LiLabAtVT/CoReg documentation built on May 8, 2022, 10:17 a.m.