inst/doc/NetSAM.R

In NetSAM: Network Seriation And Modularization

### R code from vignette source 'NetSAM.Rnw'

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### code chunk number 1: Example
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library("NetSAM")
cat("The input network can be a file.\n")
inputNetwork <- system.file("extdata","exampleNetwork.txt",package="NetSAM")
cat("The input network can be also a data object, such as graphNEL object.\n")
data(inputNetwork)
outputFileName <- paste(getwd(),"/NetSAM",sep="")
result <- NetSAM(inputNetwork, outputFileName, minModule=(-1), maxStep=4, 
method="Modularity Cutoff", ModularityThr=0.2, ZRandomNum=10, permuteNum=100, pThr=0.05)