NetGSA                  Network-based Gene Set Analysis
bic.netEst.undir        Bayesian information criterion to select the
                        tuning parameters for 'netEst.undir'
breastcancer2012        Breast cancer data from TCGA (2012).
edgelist                A data frame of edges, each row corresponding
                        to one edge
g                       A directed acyclic graph corresponding to the
                        Adrenergic signaling in cardiomyocytes pathway
                        from KEGG
group                   The vector of class indicators
netEst.dir              Constrained estimation of directed networks
netEst.undir            Constrained estimation of undirected networks
netgsa-package          Network-Based Gene Set Analysis
nonedgelist             A data frame of nonedges, each row
                        corresponding to one negative edge
pathways                A list of KEGG pathways
prepareAdjacencyMatrix
                        Construct adjacency matrices from existing
                        databases or user provided network information
preparePathways         Prepare pathway dataset needed by NetGSA
x                       Data matrix p by n
