Package index • NetPathMiner

All functions
`KGML2igraph()`	Processes KGML files into igraph objects
`stdAttrNames()` `fetchAttribute()`	MIRIAM annotation attributes
`NPMdefaults()`	Default values for NetPathMiner
`NetPathMiner-package` `NetPathMiner` `NPM`	General framework for network extraction, path mining.
`SBML2igraph()`	Processes SBML files into igraph objects
`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
`getAttrStatus()` `getAttrNames()` `getAttribute()` `setAttribute()` `rmAttribute()`	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
`layoutVertexByAttr()`	A graph layout function, which groups vertices by attribute.
`expandComplexes()` `makeGeneNetwork()`	Expand reactions / complexes into their gene constituents.
`makeMetaboliteNetwork()`	Convert metabolic network to metabolite network.
`makeReactionNetwork()`	Convert metabolic network to reaction network.
`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()` `plotClusterProbs()` `plotClusters()`	Plots the structure of all path clusters
`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.
`reindexNetwork()`	Replaces current vertex ids with chosen attribute.
`rmSmallCompounds()`	Remove uniquitous compounds from a metabolic network
`simplifyReactionNetwork()`	Removes reactions with no gene annotations
`toGraphNEL()`	Converts an annotated igraph object to graphNEL
`vertexDeleteReconnect()`	Network editing: removing vertices and connecting their neighbours

Reference

All functions