# Biological Network Analysis in R

## Documentation for package ‘BioNAR’ version 1.13.3

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

## Help Pages

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
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.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.