Reverse engineering of molecular regulatory networks with qp-graphs


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Documentation for package ‘qpgraph’ version 1.2.0

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qpgraph-package The q-order partial correlation graph learning software, qpgraph.
EcoliOxygen Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
filtered.regulon6.1 Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
gds680.eset Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
qpAnyGraph A graph
qpAvgNrr Average non-rejection rate estimation
qpAvgNrr,data.frame-method Average non-rejection rate estimation
qpAvgNrr,ExpressionSet-method Average non-rejection rate estimation
qpAvgNrr,matrix-method Average non-rejection rate estimation
qpCItest Conditional independence test
qpCItest,data.frame-method Conditional independence test
qpCItest,ExpressionSet-method Conditional independence test
qpCItest,matrix-method Conditional independence test
qpClique Complexity of the resulting qp-graphs
qpCliqueNumber Clique number
qpDscale Scale a matrix by its diagonal
qpEdgeNrr Non-rejection rate estimation for a pair of variables
qpEdgeNrr,data.frame-method Non-rejection rate estimation for a pair of variables
qpEdgeNrr,ExpressionSet-method Non-rejection rate estimation for a pair of variables
qpEdgeNrr,matrix-method Non-rejection rate estimation for a pair of variables
qpFunctionalCoherence Functional coherence estimation
qpGetCliques Clique list
qpGraph The qp-graph
qpgraph The q-order partial correlation graph learning software, qpgraph.
qpGraphDensity Densities of resulting qp-graphs
qpHist Histograms of non-rejection rates
qpI2K Random concentration matrix
qpImportNrr Import non-rejection rates
qpIPF Iterative proportional fitting algorithm
qpK2R Partial correlation coefficients
qpNrr Non-rejection rate estimation
qpNrr,data.frame-method Non-rejection rate estimation
qpNrr,ExpressionSet-method Non-rejection rate estimation
qpNrr,matrix-method Non-rejection rate estimation
qpPAC Estimation of partial correlation coefficients
qpPAC,data.frame-method Estimation of partial correlation coefficients
qpPAC,ExpressionSet-method Estimation of partial correlation coefficients
qpPAC,matrix-method Estimation of partial correlation coefficients
qpPCC Estimation of Pearson correlation coefficients
qpPCC,data.frame-method Estimation of Pearson correlation coefficients
qpPCC,ExpressionSet-method Estimation of Pearson correlation coefficients
qpPCC,matrix-method Estimation of Pearson correlation coefficients
qpPrecisionRecall Calculation of precision-recall curves
qpPRscoreThreshold Calculation of scores thresholds attaining nominal precision or recall levels
qpRndGraph Random undirected graphs with maximum connectivity degree
qpSampleMvnorm Sample multivariate normal observations