# Reverse engineering of molecular regulatory networks with qp-graphs

## Documentation for package ‘qpgraph’ version 1.12.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## 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