with β ≥ 1. The function adjacency calculates the adjacency matrix from expression data. The adjacency in Equation 5 implies that the weighted adjacency aij between two genes is proportional to their similarity on a logarithmic scale, log(aij) = β × log(sij). Adjacency functions for both weighted and unweighted networks require the user to choose threshold parameters, for example by applying the approximate scale-free topology criterion [5]. The package provides functions pickSoftThreshold, pickHardThreshold that assist in choosing the parameters, as well as the function scaleFreePlot for evaluating whether the network exhibits a scale free topology. Figure 2A shows a plot identifying scale free topology in simulated expression data.
