Routines for the functional analysis of biological networks
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Documentation for package ‘BioNet’ version 1.62.0
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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 |