A C D E F G H M N P Q R S T U V misc
| qpgraph-package | Estimation of genetic and molecular regulatory networks from high-throughput genomics data |
| addeQTL | eQTL experimental cross model class |
| addeQTL-method | eQTL experimental cross model class |
| addGeneAssociation | eQTL experimental cross model class |
| addGeneAssociation-method | eQTL experimental cross model class |
| addGenes | eQTL experimental cross model class |
| addGenes-method | eQTL experimental cross model class |
| alleQTL | eQTL network model class |
| alleQTL-method | eQTL experimental cross model class |
| alleQTL-method | eQTL network model class |
| allGeneAssociations | eQTL network model class |
| allGeneAssociations-method | eQTL network model class |
| ciseQTL | eQTL network model class |
| ciseQTL-method | eQTL experimental cross model class |
| ciseQTL-method | eQTL network model class |
| det-method | Sum of squares and deviations Matrices |
| determinant-method | Sum of squares and deviations Matrices |
| dim-method | Homogeneous mixed graphical Markov model |
| dim-method | Sum of squares and deviations Matrices |
| dim-method | Undirected Gaussian graphical Markov model |
| dimnames-method | Homogeneous mixed graphical Markov model |
| dimnames-method | Sum of squares and deviations Matrices |
| dimnames-method | Undirected Gaussian graphical Markov model |
| dRegularGraphParam | Graph parameter classes |
| dRegularGraphParam-class | Graph parameter classes |
| dRegularMarkedGraphParam | Graph parameter classes |
| dRegularMarkedGraphParam-class | Graph parameter classes |
| EcoliOxygen | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
| eQTLcross | eQTL experimental cross model class |
| eQTLcross-class | eQTL experimental cross model class |
| eQTLcross-method | eQTL experimental cross model class |
| eQTLcrossParam | eQTL experimental cross model class |
| eQTLcrossParam-class | eQTL experimental cross model class |
| eQTLnetwork | eQTL network model class |
| eQTLnetwork-class | eQTL network model class |
| eQTLnetworkEstimate | Estimation of a eQTL network from genetical genomics data |
| eQTLnetworkEstimate-method | Estimation of a eQTL network from genetical genomics data |
| eQTLnetworkEstimationParam | eQTL network parameter model class |
| eQTLnetworkEstimationParam-class | eQTL network parameter model class |
| erGraphParam | Graph parameter classes |
| erGraphParam-class | Graph parameter classes |
| erMarkedGraphParam | Graph parameter classes |
| erMarkedGraphParam-class | Graph parameter classes |
| filterCollinearities | Filter collinearities |
| filtered.regulon6.1 | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
| gds680.eset | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
| geneAnnotation | eQTL network parameter model class |
| geneAnnotation-method | eQTL network model class |
| geneAnnotation-method | eQTL network parameter model class |
| geneNames | eQTL network parameter model class |
| geneNames-method | eQTL experimental cross model class |
| geneNames-method | eQTL network model class |
| geneNames-method | eQTL network parameter model class |
| geneticMap | eQTL network parameter model class |
| geneticMap-method | eQTL network model class |
| geneticMap-method | eQTL network parameter model class |
| ggData | eQTL network parameter model class |
| ggData-method | eQTL network parameter model class |
| graph | eQTL network model class |
| graph-method | eQTL network model class |
| graphParam-class | Graph parameter classes |
| HMgmm | Homogeneous mixed graphical Markov model |
| HMgmm-class | Homogeneous mixed graphical Markov model |
| HMgmm-method | Homogeneous mixed graphical Markov model |
| markedGraphParam-class | Graph parameter classes |
| markerNames | eQTL network parameter model class |
| markerNames-method | eQTL experimental cross model class |
| markerNames-method | eQTL network model class |
| markerNames-method | eQTL network parameter model class |
| names-method | Homogeneous mixed graphical Markov model |
| names-method | Undirected Gaussian graphical Markov model |
| names-method | eQTL experimental cross model class |
| names-method | The qp-graph |
| physicalMap | eQTL network parameter model class |
| physicalMap-method | eQTL network model class |
| physicalMap-method | eQTL network parameter model class |
| plot-method | Homogeneous mixed graphical Markov model |
| plot-method | Undirected Gaussian graphical Markov model |
| plot-method | eQTL experimental cross model class |
| plot-method | eQTL network model class |
| plot-method | Graph parameter classes |
| qpAllCItests | Tests of conditional independence |
| qpAllCItests-method | Tests of conditional independence |
| qpAnyGraph | A graph |
| qpAvgNrr | Average non-rejection rate estimation |
| qpAvgNrr-method | Average non-rejection rate estimation |
| qpBoundary | Maximum boundary size of the resulting qp-graphs |
| qpCItest | Conditional independence test |
| qpCItest-method | Conditional independence test |
| qpClique | Complexity of the resulting qp-graphs |
| qpCliqueNumber | Clique number |
| qpCov | Calculation of the sample covariance matrix |
| qpEdgeCor | Non-rejection rate estimation for a pair of variables |
| qpEdgeCor-method | Non-rejection rate estimation for a pair of variables |
| qpEdgeNrr | Non-rejection rate estimation for a pair of variables |
| qpEdgeNrr-method | Non-rejection rate estimation for a pair of variables |
| qpFunctionalCoherence | Functional coherence estimation |
| qpFunctionalCoherence-method | Functional coherence estimation |
| qpG2Sigma | Random covariance matrix |
| qpGenNrr | Generalized non-rejection rate estimation |
| qpGenNrr-method | Generalized non-rejection rate estimation |
| qpGetCliques | Clique list |
| qpGraph | The qp-graph |
| qpgraph | Estimation of genetic and molecular regulatory networks from high-throughput genomics data |
| qpGraph-class | The qp-graph |
| qpGraph-method | The qp-graph |
| qpGraphDensity | Densities of resulting qp-graphs |
| 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 |
| qpNrr-method | Non-rejection rate estimation |
| qpPAC | Estimation of partial correlation coefficients |
| qpPAC-method | Estimation of partial correlation coefficients |
| qpPathWeight | Calculation of path weights |
| qpPathWeight-method | Calculation of path weights |
| qpPCC | Estimation of Pearson correlation coefficients |
| qpPCC-method | 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 or recall levels |
| 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 |
| rcmvnorm | Homogeneous mixed graphical Markov model |
| rcmvnorm-method | Homogeneous mixed graphical Markov model |
| reQTLcross | eQTL experimental cross model class |
| reQTLcross-method | eQTL experimental cross model class |
| resetCutoffs | eQTL network model class |
| resetCutoffs-method | eQTL network model class |
| rgraphBAM | Graph parameter classes |
| rgraphBAM-method | Graph parameter classes |
| rHMgmm | Homogeneous mixed graphical Markov model |
| rHMgmm-method | Homogeneous mixed graphical Markov model |
| rmvnorm | Undirected Gaussian graphical Markov model |
| rmvnorm-method | Undirected Gaussian graphical Markov model |
| rUGgmm | Undirected Gaussian graphical Markov model |
| rUGgmm-method | Undirected Gaussian graphical Markov model |
| show-method | Homogeneous mixed graphical Markov model |
| show-method | Sum of squares and deviations Matrices |
| show-method | Undirected Gaussian graphical Markov model |
| show-method | eQTL experimental cross model class |
| show-method | eQTL network model class |
| show-method | eQTL network parameter model class |
| show-method | Graph parameter classes |
| show-method | The qp-graph |
| sim.cross | eQTL experimental cross model class |
| sim.cross-method | eQTL experimental cross model class |
| SsdMatrix-class | Sum of squares and deviations Matrices |
| subset.filtered.regulon6.1 | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
| subset.gds680.eset | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
| summary-method | Homogeneous mixed graphical Markov model |
| summary-method | Undirected Gaussian graphical Markov model |
| transeQTL | eQTL experimental cross model class |
| transeQTL-method | eQTL experimental cross model class |
| UGgmm | Undirected Gaussian graphical Markov model |
| UGgmm-class | Undirected Gaussian graphical Markov model |
| UGgmm-method | Undirected Gaussian graphical Markov model |
| varExplained | eQTL network model class |
| varExplained-method | eQTL network model class |
| $-method | Homogeneous mixed graphical Markov model |
| $-method | Undirected Gaussian graphical Markov model |
| $-method | eQTL experimental cross model class |
| $-method | The qp-graph |