Routines for the functional analysis of biological networks

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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