| netgsa-package | 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 | 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 |