Man pages for BioNet
Routines for the functional analysis of biological networks

aggrPvalsAggregate several p-values into one p-value
BioNet-packageRoutines for the functional analysis of biological networks
bumOptimFitting a beta-uniform mixture model to p-value distribution
compareNetworksCompare parameters of two networks
consensusScoresCalculation of a consensus score for a network
fbumCompute the density of the bum distribution
fbumLLCalculate log likelihood of BUM model
fdrThresholdCalculate p-value threshold for given FDR
fitBumModelFit beta-uniform mixture model to a p-value distribution
getCompScoresPartition scores for subgraphs of the network
getEdgeListGet representation of graph as edgelist
hist.bumHistogram of the p-value distribution with the fitted bum...
largestCompExtract largest component of network
largestScoreCompComponent with largest score
loadNetwork.sifLoad network from Cytoscape sif file
loadNetwork.tabLoad network from tabular format
makeNetworkCreate graph from source and target vectors
mapByVarSelect probeset by variance and get PPI ID
permutateNodesPermute node labels
piUpperUpper bound pi for the fraction of noise
plot3dModule3D plot of the network
plot.bumQuantile-quantile plot for the beta-uniform mixture model
plotLLSurfaceLog likelihood surface plot
plotModulePlot of the network
print.bumPrint information about bum model
pvaluesExampleExample p-values for aggregation statistics
readHeinzGraphConvert HEINZ output to graph
readHeinzTreeConvert HEINZ output to tree
resamplingPvaluesResampling of microarray expression values and test for...
rmSelfLoopsRemove self-loops in a graph
runFastHeinzCalculate heuristically maximum scoring subnetwork
runHeinzStart HEINZ
save3dModuleSave a 3D plot of the network
saveNetworkSave undirected network in various formats
scanFDRDataframe of scores over a given range of FDRs
scoreFunctionScoring function for p-values
scoreNodesScore the nodes of a network
scoreOffsetChange score offset for 2 FDRs
sortedEdgeListGet a sorted edgelist
subNetworkCreate a subGraph
summary.bumPrint summary of informations about bum model
writeHeinzWrite input files for HEINZ
writeHeinzEdgesWrite edge input file for HEINZ
writeHeinzNodesWrite node input file for HEINZ
BioNet documentation built on Nov. 8, 2020, 5:48 p.m.