Network Centrality Metrics for Elastic-Net Regularized Models

buildLambda | Auxiliary function to generate suitable lambda parameters |

buildStringNetwork | Build gene network from peptide ids |

cv.glmDegree | GLMNET cross-validation model penalizing nodes with small... |

cv.glmHub | GLMNET cross-validation model penalizing nodes with small... |

cv.glmOrphan | GLMNET cross-validation model penalizing nodes with high... |

cv.glmSparseNet | Calculate cross validating GLM model with network-based... |

degreeCor | Calculate the degree of the correlation network based on... |

degreeCov | Calculate the degree of the covariance network based on xdata |

degreeSparsebn | Calculate degree of correlation matrix |

dot-calcPenalty | Calculate penalty based on data |

dot-degreeGeneric | Generic function to calculate degree based on data |

dot-glmSparseNetPrivate | Calculate GLM model with network-based regularization |

dot-networkGenericParallel | Calculate the upper triu of the matrix |

dot-networkWorker | Worker to calculate edge weight for each pair of ix.i node... |

ensemblGeneNames | Retrieve ensembl gene names from biomaRt |

geneNames | Retrieve gene names from biomaRt |

glmDegree | GLMNET model penalizing nodes with small degree |

glmHub | GLMNET model penalizing nodes with small degree |

glmOrphan | GLMNET model penalizing nodes with high degree |

glmSparseNet | Calculate GLM model with network-based regularization |

hallmarks | Retrieve hallmarks of cancer count for genes |

heuristicScale | Heuristic function to use in high dimensions |

hubHeuristic | Heuristic function to penalize nodes with low degree |

networkCorParallel | Calculates the correlation network |

networkCovParallel | Calculates the covariance network |

networkOptions | Setup network options |

orphanHeuristic | Heuristic function to penalize nodes with high degree |

protein2EnsemblGeneNames | Retrieve ensembl gene ids from proteins |

separate2GroupsCox | Separate data in High and Low risk groups (based on Cox... |

stringDBhomoSapiens | Download protein-protein interactions from STRING DB |

string.network.700.cache | Cache of protein-protein network, as it takes some time to... |

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