Deciphering Biological Networks with Patterned Heterogeneous Measurements

analyze_network-methods | Analysing the network |

as.micro_array | Coerce a matrix into a micro_array object. |

CascadeFinit | Create initial F matrices for cascade networks inference. |

CascadeFshape | Create F matrices shaped for cascade networks inference. |

CLL | Expression data from healthy and malignant (chronic... |

clustExploration-methods | A function to explore a dataset and cluster its rows. |

clustInference-methods | A function to explore a dataset and cluster its rows. |

compare-methods | Some basic criteria of comparison between actual and inferred... |

cutoff-methods | Choose the best cutoff |

dim-methods | Dimension of the data |

evolution-methods | See the evolution of the network with change of cutoff |

gene_expr_simulation | Simulates microarray data based on a given network. |

geneNeighborhood-methods | Find the neighborhood of a set of nodes. |

genePeakSelection-methods | Methods for selecting genes |

head-methods | Overview of a micro_array object |

IndicFinit | Create initial F matrices using specific intergroup actions... |

IndicFshape | Create F matrices using specific intergroup actions for... |

inference-methods | Reverse-engineer the network |

infos | Details on some probesets of the affy_hg_u133_plus_2... |

M | Simulated microarray. |

micro_array-class | Class '"micro_array"' |

micropred-class | Class '"micropred"' |

Net | Simulated network for examples. |

Net_inf_PL | Reverse-engineered network of the M and Net simulated data. |

network | A example of an inferred network (4 groups case). |

network2gp | A example of an inferred cascade network (2 groups case). |

networkCascade | A example of an inferred cascade network (4 groups case). |

network-class | Class '"network"' |

network_random | Generates a network. |

Patterns-package | The Patterns Package |

plotF | Plot functions for the F matrices. |

plot-methods | Plot |

position | Retrieve network position for consistent plotting. |

position-methods | Returns the position of edges in the network |

predict-methods | Methods for Function 'predict' |

print-methods | ~~ Methods for Function 'print' ~~ |

probeMerge | Function to merge probesets |

replaceBand | Replace matrix values by band. |

replaceDown | Replace matrix values triangular lower part and by band for... |

replaceUp | Replace matrix values triangular upper part and by band for... |

Selection | Selection of genes. |

summary-methods | ~~ Methods for Function 'summary' ~~ |

unionMicro-methods | Makes the union between two micro_array objects. |

unsupervised_clustering | Cluster a micro_array object: performs the clustering. |

unsupervised_clustering_auto_m_c | Cluster a micro_array object: determine optimal fuzzification... |

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