The function calculates the 1st, 2nd and 3rd order connectivities for all genes
cal_connectivity(so, m = 10, niter = 100)SiFINeT object with conn (absolute network connectivities) updated.
a SiFINeT object
number of neighbors sampled each time for the calculation of 3rd order connectivity
number of samples created for the calculation of 3rd order connectivity
For gene i, First order connectivity is defined as the number of edges connected to gene i (degree of the gene node i in the network). Second order connectivity is defined as the proportion of edges between the neighbors of gene i, calculated as number of observed edges between the neighbors of gene i divided by the number of possible edges between the neighbors. Third order connectivity is defined as a weighted proportion of edges between neighbors and neighbors of neighbors of gene i. Third order connectivity is calculated as the mean of edge proportions across weighted samples. Each gene is weighted by the number of edges it has with the neighbors of gene i. Then SiFINeT repeatedly samples m genes for niter times. For each sample, the edge proportion (number of observed edges / number of possible edges) is calculated. And the mean edge proportion across the sample is the 3rd order connectivity for gene i.