addEdgeAtts             Copy edge attributes from one graph to another
annotateGeneNames       Annotate Human Gene Names
annotateGoBP            Add GO BP annotation to the graph vertices
annotateGoCC            Add GO CC annotation to the graph vertices
annotateGoMF            Add GO MF annotation to the graph vertices
annotateGOont           Annotate nodes with GO terms
annotateInterpro        Add InterPro Family and Domain annotation to
                        the graph vertices
annotatePresynaptic     Add presynaptic functional groups
annotateSCHanno         Add SCHanno synaptic functional groups
annotateTopOntoOVG      Annotate graph with disease terms
annotateVertex          Generic annotation function
applpMatrixToGraph      Add attributes to the vertex.
BioNAR                  BioNAR: Biological Network Analysis in R
buildNetwork            Build network from data.table
calcAllClustering       Calculate memberships for all clustering
                        algorithms and store them on the graph
                        vertices.
calcBridgeness          Helper function that uses 'getBridgeness' to
                        calculate graph node bridgeness values for
                        selected algorithm and consensus matrix and
                        save them as a graph attribute
                        'BRIDGENESS.<alg>' with '<alg>' replaced by the
                        selected algorithm name.
calcCentrality          Calculate the vertex centrality measures
calcCentralityExternalDistances
                        Function to calculate a distance matrix between
                        a list of permuted vertex centrality matrices
                        and a unperturbed reference matrix.
calcCentralityInternalDistances
                        Function calculates a set of distance metrics
                        between each vertex pair given a list of vertex
                        centrality matrices
calcClustering          Calculate community membership for given
                        clustering algorithm and store the results as
                        new vertex attributes in the graph..
calcDiseasePairs        Calculate each disease-disease pair overlap
                        given a list of disease terms.
calcEntropy             Calculate the graph entropy for each perturbed
                        vertex, and save the results as new vertex
                        attributes in the graph.
calcMembership          Calculate cluster memberships for the graph.
calcReclusterMatrix     Hierarchical graph clustering
calcSparsness           Calculate sparsness of the graph.
clusteringSummary       Matrix of cluster characteristics
clusterORA              Calculate annotation enrichment for clusters in
                        the graph
compMembership          Calculate cluster memberships for one of the
                        graph component.
degreeBinnedGDAs        Prepare mapping for degree-aware annotation
                        shuffling.
diseasome               Barabasi's Diseasome Network
escapeAnnotation        Escapes elements of list in annotation.
evalCentralitySignificance
                        Compare distance distributions of internal and
                        external distances
findLCC                 Find Largest Connected Component of the graph
fitDegree               Fit Power Law to degree distribution.
fitSigmoid              Fit Fold-enrichment distribution to sigmoid
                        function
flatfile_human_gene2HDO.csv
                        Human Gene Disease Associations (GDA)
flatfile.go.BP.csv      Annotation from Gene Ontology Biological
                        Process (GO_BP)
flatfile.go.CC.csv      Annotation from Gene Ontology Cellular
                        Compartment (GO_CC)
flatfile.go.MF.csv      Annotation from Gene Ontology Molecular
                        Function (GO_MF)
getAnnotationList       Extract unique values from annotations.
getAnnotationVertexList
                        Return vertex list for each term in annotation
                        attribute
getBridgeness           Calculate bridginess from consensus matrix
getCentralityMatrix     Calculate centrality measures for graph nodes.
getClustering           Get clustering results for the graph.
getClusterSubgraphByID
                        Return induced subgraph for cluster
getCommunityGraph       Create new graph with communities as a nodes.
getDiseases             Get HDO disease IDs
getDType                Get DiseaseTypes
getDYNAMO               Calculate DYNAMO sensitivity matrix.
getEntropy              Calculates vertex perturbation graph entropy.
getEntropyRate          Calculate the maximum entropy rate and initial
                        entropy rate .
getGNP                  Generate random graph from reference
getGraphCentralityECDF
                        Convert centrality matrix into ECDF
getIDs                  Utility function to get vertex ids from vertex
                        attributes The function obtain attribute values
                        and check duplicates in it. It fails if any
                        duplicate found.
getPA                   Generate random graph from reference
getRandomGraphCentrality
                        Centrality measures for random graphs induced
                        by input one
getRobustness           Calculate cluster robustness from consensus
                        matrix
gofs                    Goodnes of fit KS test
law-class               Result of PawerLaw fit
layoutByCluster         Calculate layout based upon membership
layoutByRecluster       Calculate two-level layout from recluster
                        matrix
makeConsensusMatrix     Function to make random resampling consensus
                        matrix in memory
makeMembership          Create membership 'data.frame' from graph for
                        arbitrary annotation
markBowTie              Calculates bow-tie decomposition and marks
                        vertices with one of the following in the
                        'BowTie' attribute: • SCC - maximal strong
                        connected component; • IN - vertices not in
                        SCC, but SCC is reachable from them; • OUT -
                        vertices not in SCC, but reachable from SCC; •
                        TU - vertices not in all three above, but
                        reachable from IN and OUT is reachable from
                        them (TUBES); • IDR - vertices not in SCC, but
                        they are reachable from IN and OUT is NOT
                        reachable from them (INTENDRILS); • ODR -
                        vertices not is SCC, but they are NOT reachable
                        from IN and OUT is reachable from them
                        (OUTTENDRILS); • OTR - all other vertices.
metlMatrix              Convert sparce matrix into triplet
                        'data.frame'.
normModularity          Calculates the normalised network modularity
                        value.
permute                 Randomly shuffle annotations
plotBridgeness          Plot Bridgeness values
plotEntropy             Plot graph entropy values versus vertex degree
                        for each perturbed vertex value.
plotRatio               Plot fraction of enriched communities
plotSigmoid             Plot results of the sigmoid fit
PPI_Presynaptic.csv     Table of protein protein interactions for
                        presynaptic compartment
PPI_Presynaptic.gml     PPI graph for presynaptic compartment
prepareGDA              Function to return vertex annotation from a
                        graph in the Vertex Annotation form and format
                        it for further analysis.
PresynAn.csv            Presynaptic genes specific functional
                        annotation
recluster               Hierarchical graph clustering
removeVertexTerm        Remove vertex property.
runPermDisease          Calculate disease-disease pair overlaps on
                        permuted network to estimate its statistical
                        significance
sampleDegBinnedGDA      Function to randomly shuffle vertex annotation
                        terms, whilst preserving the vertex degree
                        originally found with that annotation term..
sampleGraphClust        Perturbe graph and calculate its clustering
SCH_flatfile.csv        Schizopherina related synaptic gene functional
                        annotation.
summaryStats            Calculate summary statistics from enrichment
                        table
unescapeAnnotation      Unescape annotation strings
zeroNA                  Auxiliary function to replace NAs with zeros.
