computeAuROC: compute AUC and ROC for the network

In LiLabAtVT/CoReg: Identification of co-regulators

compute AUC and ROC for the network

Description

This function performs the same rewiring simulation as netSimAndEval. But computes the AUC and ROC as the result

Usage

computeAuROC(g,nDup,dDup,rewProb,simMethods,steps = 2, nThreads=1)
  ## S3 method for class 'CoReg.auROC'
print(CoReg.auROC)
  ## S3 method for class 'CoReg.auROC'
summary(CoReg.auROC)
  ## S3 method for class 'CoReg.auROC'
plot(CoReg.auROC)

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 numeric value specifying the rewiring probability
simMethods	similarity indices used. Available options are: "jaccard" (jaccard similarity index),"geometric" (geometric similarity index),"invlogweighted" (inverse log weighted similarity index), "wt" (walk-trap-based similarity index)
steps	Number of steps for random walks, which is used by walk trap algorithm. Only valid when simMethods = "wt". Default value = 2
nThreads	number of threads for running the simulation. Only valid when simMethods = "geometric"
CoReg.auROC	CoReg.auROC object

Details

This function performes the rewring simulation similar to netSimAndEval, but uses the AUC values and ROC curves as the evaluation metrics. ROC curves can be plotted using the generic function plot().

Value

An object of class CoReg.auROC

Author(s)

Qi Song

See Also

rewSim

Examples

data(athNet)
re <- computeAuROC(athNet,nDup=50,dDup=10,rewProb=0.5,simMethods=c("jaccard","geometric","invlogweighted","wt"),steps = 2, nThreads=1)

# Display summary information for rewiring simulation
print(re)

# Plot ROC curves for the result
plot(re)

# Get the AUC values for the result
re$AUC

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