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qpgraph (version 2.6.1)
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Description
Estimate gene and eQTL networks from high-throughput expression and genotyping assays.
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Version
2.6.1
2.4.0
2.2.3
2.0.5
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Version
2.6.1
License
GPL (>= 2)
Maintainer
Robert Castelo
Last Published
January 1st, 1970
Functions in qpgraph (2.6.1)
Search functions
qpAllCItests
Tests of conditional independence
eQTLnetworkEstimationParam-class
eQTL network parameter model class
qpClique
Complexity of the resulting qp-graphs
qpEdgeNrr
Non-rejection rate estimation for a pair of variables
qpPCC
Estimation of Pearson correlation coefficients
qpHTF
Hastie Tibshirani Friedman iterative regression algorithm
qpImportNrr
Import non-rejection rates
qpAnyGraph
A graph
qpUnifRndAssociation
Uniformly random association values
qpAvgNrr
Average non-rejection rate estimation
SsdMatrix-class
Sum of squares and deviations Matrices
qpG2Sigma
Random covariance matrix
UGgmm-class
Undirected Gaussian graphical Markov model
qpCov
Calculation of the sample covariance matrix
qpCliqueNumber
Clique number
qpgraph-package
The q-order partial correlation graph learning software, qpgraph.
qpTopPairs
Report pairs of variables
qpIPF
Iterative proportional fitting algorithm
qpPAC
Estimation of partial correlation coefficients
qpPlotNetwork
Plots a graph
qpGenNrr
Generalized non-rejection rate estimation
qpCItest
Conditional independence test
qpNrr
Non-rejection rate estimation
eQTLnetworkEstimate
Estimation of a eQTL network from genetical genomics data
qpPrecisionRecall
Calculation of precision-recall curves
qpGraph-class
The qp-graph
qpRndWishart
Random Wishart distribution
qpUpdateCliquesRemoving
Update clique list when removing one edge
qpBoundary
Maximum boundary size of the resulting qp-graphs
qpPathWeight
Calculation of path weights
qpRndGraph
Undirected random d-regular graphs
graphParam-class
Graph parameter classes
eQTLcross-class
eQTL experimental cross model class
HMgmm-class
Homogeneous mixed graphical Markov model
qpHist
Histograms of non-rejection rates
qpK2ParCor
Partial correlation coefficients
EcoliOxygen
Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
eQTLnetwork-class
eQTL network model class
qpGraphDensity
Densities of resulting qp-graphs
qpFunctionalCoherence
Functional coherence estimation
qpPlotMap
Plots a map of associated pairs
qpPRscoreThreshold
Calculation of scores thresholds attaining nominal precision or recall levels
qpGetCliques
Clique list