Reverse engineering of molecular regulatory networks with qp-graphs

[Up] [Top]

Documentation for package ‘qpgraph’ version 1.10.1

Help Pages

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-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
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 The q-order partial correlation graph learning software, qpgraph.
qpGraphDensity Densities of resulting qp-graphs
qpHist Histograms of non-rejection rates
qpHTF Hastie Tibshirani Friedman 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
qpPCC Estimation of Pearson correlation coefficients
qpPCC-method Estimation of Pearson correlation coefficients
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
qpRndHMGM Random homogeneous mixed graphical Markov model
qpRndWishart Random Wishart distribution
qpSampleFromHMGM Sample from homogeneous mixed graphical Markov models
qpTopPairs Report pairs of variables
qpUnifRndAssociation Uniformly random association values
qpUpdateCliquesRemoving Update clique list when removing one edge