A Toolset for the Functional Analysis and Interactive Visualization of Protein Complex Data

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Documentation for package ‘ComplexMap’ version 2.0.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

benchmarkParameters	Benchmark Complex Refinement Parameters
buildComplexNetwork	Build a Complex-Complex Interaction Network
computeMapTopology	Compute Network Topology and Layout Coordinates
createComplexMap	Create a Complete Complex Map Object
demoComplexes	Example Protein Complex List
evaluateComplexes	Evaluate Predicted Protein Complexes Against a Reference Set
explore	Explore a ComplexMap Object Interactively
exportNetwork	Export a ComplexMap Network for External Tools
generateNodeAttributes	Generate Node Attributes for a Complex Network
getEdgeTable	Get the Edge Table from a ComplexMap Object
getExampleGmt	Get the Path to an Example GMT File
getGmtFromFile	Read a GMT File from a Local Path
getGoGmt	Fetch Gene Ontology (GO) Gene Sets
getMsigdbGmt	Fetch Gene Sets from MSigDB
getNodeTable	Get the Node Table from a ComplexMap Object
getReactomeGmt	Fetch Reactome Pathway Gene Sets
print.ComplexMap	Print Method for a ComplexMap Object
pruneNetwork	Prune Network Edges Before Cytoscape Export
qcComplexList	Perform Quality Control on a List of Protein Complexes
queryMap	Query a ComplexMap Object
referenceComplexes	Reference Protein Complex Set (CORUM)
refineComplexList	Refine a List of Protein Complexes by Size and Redundancy
runComplexEnrichment	Run Gene Set Enrichment Analysis on a List of Complexes
runComplexMapApp	Run the ComplexMap Interactive Explorer
scaleLayoutForCytoscape	Scale Layout Coordinates for Cytoscape.js
toCytoscapeJSON	Export a ComplexMap Object to Cytoscape.js JSON