Routines for the functional analysis of biological networks


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Documentation for package ‘BioNet’ version 1.29.1

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BioNet-package Routines for the functional analysis of biological networks
aggrPvals Aggregate several p-values into one p-value
BioNet Routines for the functional analysis of biological networks
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