Estimation of genetic and molecular regulatory networks from high-throughput genomics data

EcoliOxygen | Preprocessed microarray oxygen deprivation data and filtered... |

eQTLcross-class | eQTL experimental cross model class |

eQTLnetwork-class | eQTL network model class |

eQTLnetworkEstimate | Estimation of a eQTL network from genetical genomics data |

eQTLnetworkEstimationParam-class | eQTL network parameter model class |

graphParam-class | Graph parameter classes |

HMgmm-class | Homogeneous mixed graphical Markov model |

qpAllCItests | Tests of conditional independence |

qpAnyGraph | A graph |

qpAvgNrr | Average non-rejection rate estimation |

qpBoundary | Maximum boundary size of the resulting qp-graphs |

qpCItest | Conditional independence test |

qpClique | Complexity of the resulting qp-graphs |

qpCliqueNumber | Clique number |

qpCov | Calculation of the sample covariance matrix |

qpEdgeNrr | Non-rejection rate estimation for a pair of variables |

qpFunctionalCoherence | Functional coherence estimation |

qpG2Sigma | Random covariance matrix |

qpGenNrr | Generalized non-rejection rate estimation |

qpGetCliques | Clique list |

qpGraph-class | The qp-graph |

qpGraphDensity | Densities of resulting qp-graphs |

qpgraph-package | Estimation of genetic and molecular regulatory networks from... |

qpHist | Histograms of non-rejection rates |

qpHTF | Hastie Tibshirani Friedman iterative regression algorithm |

qpImportNrr | Import non-rejection rates |

qpIPF | Iterative proportional fitting algorithm |

qpK2ParCor | Partial correlation coefficients |

qpNrr | Non-rejection rate estimation |

qpPAC | Estimation of partial correlation coefficients |

qpPathWeight | Calculation of path weights |

qpPCC | Estimation of Pearson correlation coefficients |

qpPlotMap | Plots a map of associated pairs |

qpPlotNetwork | Plots a graph |

qpPrecisionRecall | Calculation of precision-recall curves |

qpPRscoreThreshold | Calculation of scores thresholds attaining nominal precision... |

qpRndGraph | Undirected random d-regular graphs |

qpRndWishart | Random Wishart distribution |

qpTopPairs | Report pairs of variables |

qpUnifRndAssociation | Uniformly random association values |

qpUpdateCliquesRemoving | Update clique list when removing one edge |

SsdMatrix-class | Sum of squares and deviations Matrices |

UGgmm-class | Undirected Gaussian graphical Markov model |

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