NetPathMiner for Biological Network Construction, Path Mining and Visualization

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Documentation for package ‘NetPathMiner’ version 1.24.0

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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
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