# Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data

## Documentation for package ‘qpgraph’ version 2.44.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- A --

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

## -- C --

ciseQTL | eQTL network model class
ciseQTL-method | eQTL experimental cross model class
ciseQTL-method | eQTL network model class

## -- D --

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

## -- E --

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

## -- F --

filterCollinearities | Filter collinearities
filtered.regulon6.1 | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data

## -- G --

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

## -- H --

HMgmm | Homogeneous mixed graphical Markov model
HMgmm-class | Homogeneous mixed graphical Markov model
HMgmm-method | Homogeneous mixed graphical Markov model

## -- M --

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

## -- N --

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

## -- P --

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

## -- Q --

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

## -- R --

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

## -- S --

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

## -- T --

transeQTL | eQTL experimental cross model class
transeQTL-method | eQTL experimental cross model class

## -- U --

UGgmm | Undirected Gaussian graphical Markov model
UGgmm-class | Undirected Gaussian graphical Markov model
UGgmm-method | Undirected Gaussian graphical Markov model

## -- V --

varExplained | eQTL network model class
varExplained-method | eQTL network model class

## -- misc --

$-method | Homogeneous mixed graphical Markov model
$-method | Undirected Gaussian graphical Markov model
$-method | eQTL experimental cross model class
$-method | The qp-graph