NetPathMiner for Biological Network Construction, Path Mining and Visualization

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Documentation for package ‘NetPathMiner’ version 1.42.0

• 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.
makeMetaboliteNetwork	Convert metabolic network to metabolite network.
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
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.
rmAttribute	Get / Set vertex attribute names and coverage
rmSmallCompounds	Remove uniquitous compounds from a metabolic 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