Man pages for ahmohamed/NetPathMiner
NetPathMiner for Biological Network Construction, Path Mining and Visualization
| assignEdgeWeights | Assigning weights to network edges |
| biopax2igraph | Processes BioPAX objects into igraph objects |
| colorVertexByAttr | Computes colors for vertices according to their attributes. |
| ex_biopax | Biopax example data |
| ex_kgml_sig | Singaling network from KGML example |
| ex_microarray | An microarray data example. |
| ex_sbml | Metabolic network from SBML example |
| extractPathNetwork | Creates a subnetwork from a ranked path list |
| getAttr | Get / Set vertex attribute names and coverage |
| getGeneSetNetworks | Generate geneset networks from an annotated network. |
| getGeneSets | Generate genesets from an annotated network. |
| getPathsAsEIDs | Convert a ranked path list to edge ids of a graph |
| KGML2igraph | Processes KGML files into igraph objects |
| layoutVertexByAttr | A graph layout function, which groups vertices by attribute. |
| makeGeneNetwork | Expand reactions / complexes into their gene constituents. |
| makeMetaboliteNetwork | Convert metabolic network to metabolite network. |
| makeReactionNetwork | Convert metabolic network to reaction network. |
| MIRIAM | MIRIAM annotation attributes |
| NetPathMiner-package | General framework for network extraction, path mining. |
| NPMdefaults | Default values for NetPathMiner |
| pathClassifier | HME3M Markov pathway classifier. |
| pathCluster | 3M Markov mixture model for clustering pathways |
| pathRanker | Extracting and ranking paths from a network |
| pathsToBinary | Converts the result from pathRanker into something suitable... |
| plotAllNetworks | Higlighting ranked paths over multiple network... |
| plotClassifierROC | Diagnostic plots for pathClassifier. |
| plotClusters | Plots the structure of all path clusters |
| plotCytoscape | Plots an annotated igraph object in Cytoscape. |
| plotNetwork | Plots an annotated igraph object. |
| plotPathClassifier | Plots the structure of specified path found by... |
| plotPathCluster | Plots the structure of specified path cluster |
| plotPaths | Plots an annotated igraph object higlighting ranked paths. |
| predictPathClassifier | Predicts new paths given a pathClassifier model. |
| predictPathCluster | Predicts new paths given a pathCluster model |
| registerMemoryErr | Internal method to register memery errors. |
| reindexNetwork | Replaces current vertex ids with chosen attribute. |
| rmSmallCompounds | Remove uniquitous compounds from a metabolic network |
| SBML2igraph | Processes SBML files into igraph objects |
| simplifyReactionNetwork | Removes reactions with no gene annotations |
| toGraphNEL | Converts an annotated igraph object to graphNEL |
| vertexDeleteReconnect | Network editing: removing vertices and connecting their... |
