NetGSA                  Network-based Gene Set Analysis
NetGSAq                 "Quick" Network-based Gene Set Analysis
bic.netEst.undir        Bayesian information criterion to select the
                        tuning parameters for 'netEst.undir'
breastcancer2012_subset
                        Breast cancer data from TCGA (2012). This is a
                        750 gene subset
edgelist                A data frame of edges, each row corresponding
                        to one edge
formatPathways          Format cytoscape nested networks
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
obtainClusters          Estimate optimal gene clustering structure
obtainEdgeList          Obtain edgelist from graphite databases. To be
                        used within prepareAdjMat
pathways                A list of KEGG pathways
pathways_mat            Matrix with pathway indicators
plot.NetGSA             Generates NetGSA plots
prepareAdjMat           Construct adjacency matrices from graphite
                        databases and/or user provided network
                        information
stackDatabases          Combine edges from databases into a data.table
x                       Data matrix p by n
zoomPathway             Zoom in on pathway in igraph
