Biological Network Analysis in R

Documentation for package ‘BioNAR’ version 1.9.1

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BioNAR-package	BioNAR: Biological Network Analysis in R
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
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.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)
flatfile_human_gene2HDO.csv	Human Gene Disease Associations (GDA)
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.