# NetPathMiner for Biological Network Construction, Path Mining and Visualization

## Documentation for package ‘NetPathMiner’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

NetPathMiner-package | General framework for network extraction, path mining.
assignEdgeWeights | Assigning weights to network edges
biopax2igraph | Processes BioPAX objects into igraph objects
colorVertexByAttr | Computes colors for vertices according to their attributes.
expandComplexes | Expand reactions / complexes into their gene constituents.
extractPathNetwork | Creates a subnetwork from a ranked path list
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
fetchAttribute | MIRIAM annotation attributes
getAttribute | Get / Set vertex attribute names and coverage
getAttrNames | Get / Set vertex attribute names and coverage
getAttrStatus | 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.
makeReactionNetwork | Convert metabolic network to reaction network.
NetPathMiner | General framework for network extraction, path mining.
NPM | 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 for pathClassifier or pathCluster.
plotAllNetworks | Higlighting ranked paths over multiple network representations.
plotClassifierROC | Diagnostic plots for pathClassifier.
plotClusterMatrix | Plots the structure of all path clusters
plotClusterProbs | Plots the structure of all path clusters
plotClusters | Plots the structure of all path clusters
plotCytoscape | Plots an annotated igraph object in Cytoscape.
plotCytoscapeGML | Plots an annotated igraph object in Cytoscape.
plotNetwork | Plots an annotated igraph object.
plotPathClassifier | Plots the structure of specified path found by pathClassifier.
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.
rmAttribute | Get / Set vertex attribute names and coverage
rmSmallCompounds | Remove uniquitous compounds from a metabolic network
samplePaths | Creates a set of sample path p-values for each length given a weighted network
SBML2igraph | Processes SBML files into igraph objects
setAttribute | Get / Set vertex attribute names and coverage
simplifyReactionNetwork | Removes reactions with no gene annotations
stdAttrNames | MIRIAM annotation attributes
toGraphNEL | Converts an annotated igraph object to graphNEL
vertexDeleteReconnect | Network editing: removing vertices and connecting their neighbours