Estimation of genetic and molecular regulatory networks from high-throughput genomics data

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Documentation for package ‘qpgraph’ version 2.38.0

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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