BioNet-package          Routines for the functional analysis of
                        biological networks
aggrPvals               Aggregate several p-values into one p-value
bumOptim                Fitting a beta-uniform mixture model to p-value
                        distribution
compareNetworks         Compare parameters of two networks
consensusScores         Calculation of a consensus score for a network
fbum                    Compute the density of the bum distribution
fbumLL                  Calculate log likelihood of BUM model
fdrThreshold            Calculate p-value threshold for given FDR
fitBumModel             Fit beta-uniform mixture model to a p-value
                        distribution
getCompScores           Partition scores for subgraphs of the network
getEdgeList             Get representation of graph as edgelist
hist.bum                Histogram of the p-value distribution with the
                        fitted bum model
largestComp             Extract largest component of network
largestScoreComp        Component with largest score
loadNetwork.sif         Load network from Cytoscape sif file
loadNetwork.tab         Load network from tabular format
makeNetwork             Create graph from source and target vectors
mapByVar                Select probeset by variance and get PPI ID
permutateNodes          Permute node labels
piUpper                 Upper bound pi for the fraction of noise
plot.bum                Quantile-quantile plot for the beta-uniform
                        mixture model
plot3dModule            3D plot of the network
plotLLSurface           Log likelihood surface plot
plotModule              Plot of the network
print.bum               Print information about bum model
pvaluesExample          Example p-values for aggregation statistics
readHeinzGraph          Convert HEINZ output to graph
readHeinzTree           Convert HEINZ output to tree
resamplingPvalues       Resampling of microarray expression values and
                        test for differential expression.
rmSelfLoops             Remove self-loops in a graph
runFastHeinz            Calculate heuristically maximum scoring
                        subnetwork
runHeinz                Start HEINZ
save3dModule            Save a 3D plot of the network
saveNetwork             Save undirected network in various formats
scanFDR                 Dataframe of scores over a given range of FDRs
scoreFunction           Scoring function for p-values
scoreNodes              Score the nodes of a network
scoreOffset             Change score offset for 2 FDRs
sortedEdgeList          Get a sorted edgelist
subNetwork              Create a subGraph
summary.bum             Print summary of informations about bum model
writeHeinz              Write input files for HEINZ
writeHeinzEdges         Write edge input file for HEINZ
writeHeinzNodes         Write node input file for HEINZ
