### R code from vignette source 'NetSAM.Rnw' ################################################### ### code chunk number 1: Example ################################################### 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)