Man pages for drjingma/netgsa
Network-Based Gene Set Analysis
| addUserEdges | Add user edgelist to edgelist found in graphite |
| bic.netEst.undir | Bayesian information criterion to select the tuning... |
| breastcancer2012 | Breast cancer data from TCGA (2012). |
| checkUserEdges | Check user edgelist for errors |
| convertEdgeListToZeroOne | Convert edgelist and list of non-edges to zero/one adjacency... |
| edgelist | A data frame of edges, each row corresponding to one edge |
| formatPathways | Format cytoscape nested networks |
| group | The vector of class indicators |
| netEstClusts | Estimates network for each cluster |
| netEst.dir | Constrained estimation of directed networks |
| netEst.undir | Constrained estimation of undirected networks |
| NetGSA | Network-based Gene Set Analysis |
| netgsa-package | Network-Based Gene Set Analysis |
| NetGSAq | "Quick" Network-based Gene Set Analysis |
| nonedgelist | A data frame of nonedges, each row corresponding to one... |
| obtainClusters | Estimate optimal gene clustering structure |
| obtainEdgeList | Obtain edgelist from graphite databases. To be used within... |
| 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... |
| preparePathways | Prepare pathway dataset needed by NetGSA |
| stackDatabases | Combine edges from databases into a data.table |
| x | Data matrix p by n |
| zoomPathway | Zoom in on pathway in igraph |
