aggrPvals | Aggregate several p-values into one p-value |
BioNet-package | 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... |
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 |
plot3dModule | 3D plot of the network |
plot.bum | Quantile-quantile plot for the beta-uniform mixture model |
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... |
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 |
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