Man pages for topherconley/spacemap
A novel conditional graphical model for integrative genomics
| adj2igraph | Convert adjacency matrix to igraph with annotations. |
| adjacency | Adjacency matrix from spacemap and spacemap models |
| algoFDR | False discovery rate |
| algoMCC | Matthew's Correlation Coefficient (MCC) |
| algoPower | Power function |
| bcpls | Network toolkit example input data |
| bicCondLike | BIC for space under conditional chain graph likelihood... |
| bicLike | BIC for space under likelihood setting. |
| bootEnsemble | Ensemble networks through boostrapping. |
| bootVote | Model aggregation through Boot.Vote |
| cisTrans | Identify x-y cis and trans edges. |
| cvPerf | CV.Vote Model Performance |
| cvVote | Cross validation (CV.Vote) for spacemap and space models. |
| initFit | Identify scale of tuning parameters. |
| modEnrich | Module enrichment analysis. |
| nonZeroUpper | Count the number of y-y edges |
| nonZeroWhole | Count the number of x-y edges |
| rankHub | Prioritize networks hubs by degree. |
| reportHubs | Report top hub nodes with attributes. |
| reportJointPerf | Report joint performance of (x-y,y-y) edge detection |
| reportPerf | Report performance of x-y or y-y edge detection |
| sim1 | Toy Hub Network Simulation |
| space | Fit the SPACE model. |
| spacemap | Fit the spacemap model. |
| tuneVis | Visualize cross validation metrics |
| xHubEnrich | Functional enrichment of x-hub neighborhood. |
