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

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Author
Robert Castelo [aut, cre], Alberto Roverato [aut]
Date of publication
None
Maintainer
Robert Castelo <robert.castelo@upf.edu>
License
GPL (>= 2)
Version
2.8.1
URLs

View on Bioconductor

Man pages

EcoliOxygen
Preprocessed microarray oxygen deprivation data and filtered...
eQTLcross-class
eQTL experimental cross model class
eQTLnetwork-class
eQTL network model class
eQTLnetworkEstimate
Estimation of a eQTL network from genetical genomics data
eQTLnetworkEstimationParam-class
eQTL network parameter model class
graphParam-class
Graph parameter classes
HMgmm-class
Homogeneous mixed graphical Markov model
qpAllCItests
Tests of conditional independence
qpAnyGraph
A graph
qpAvgNrr
Average non-rejection rate estimation
qpBoundary
Maximum boundary size of the resulting qp-graphs
qpCItest
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
qpFunctionalCoherence
Functional coherence estimation
qpG2Sigma
Random covariance matrix
qpGenNrr
Generalized non-rejection rate estimation
qpGetCliques
Clique list
qpGraph-class
The qp-graph
qpGraphDensity
Densities of resulting qp-graphs
qpgraph-package
The q-order partial correlation graph learning software,...
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
qpPAC
Estimation of partial correlation coefficients
qpPathWeight
Calculation of path weights
qpPCC
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...
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
SsdMatrix-class
Sum of squares and deviations Matrices
UGgmm-class
Undirected Gaussian graphical Markov model

Files in this package

qpgraph/DESCRIPTION
qpgraph/NAMESPACE
qpgraph/NEWS
qpgraph/R
qpgraph/R/AllClass.R
qpgraph/R/AllGeneric.R
qpgraph/R/Defunct.R
qpgraph/R/HMgmm-methods.R
qpgraph/R/SsdMatrix.R
qpgraph/R/UGgmm-methods.R
qpgraph/R/eQTLcross-methods.R
qpgraph/R/eQTLnetwork-methods.R
qpgraph/R/eQTLnetworkEstimate.R
qpgraph/R/eQTLnetworkEstimationParam-methods.R
qpgraph/R/graphParam-methods.R
qpgraph/R/qpCItest.R
qpgraph/R/qpGraph-methods.R
qpgraph/R/qpSimulate.R
qpgraph/R/qpgraph.R
qpgraph/R/zzz.R
qpgraph/build
qpgraph/build/vignette.rds
qpgraph/cleanup
qpgraph/configure
qpgraph/configure.ac
qpgraph/data
qpgraph/data/EcoliOxygen.RData
qpgraph/data/datalist
qpgraph/inst
qpgraph/inst/CITATION
qpgraph/inst/doc
qpgraph/inst/doc/BasicUsersGuide.pdf
qpgraph/inst/doc/eQTLnetworks.R
qpgraph/inst/doc/eQTLnetworks.Rnw
qpgraph/inst/doc/eQTLnetworks.pdf
qpgraph/inst/doc/qpTxRegNet.R
qpgraph/inst/doc/qpTxRegNet.Rnw
qpgraph/inst/doc/qpTxRegNet.pdf
qpgraph/inst/doc/qpgraphSimulate.R
qpgraph/inst/doc/qpgraphSimulate.Rnw
qpgraph/inst/doc/qpgraphSimulate.pdf
qpgraph/inst/snow
qpgraph/inst/snow/RMPInode.R
qpgraph/inst/snow/RNWSnode.R
qpgraph/inst/snow/RPVMnode.R
qpgraph/inst/snow/RSOCKnode.R
qpgraph/inst/unitTests
qpgraph/inst/unitTests/test_qpCItest.R
qpgraph/inst/unitTests/test_qpNrr.R
qpgraph/inst/unitTests/test_rgraphBAM.R
qpgraph/man
qpgraph/man/EcoliOxygen.Rd
qpgraph/man/HMgmm-class.Rd
qpgraph/man/SsdMatrix-class.Rd
qpgraph/man/UGgmm-class.Rd
qpgraph/man/eQTLcross-class.Rd
qpgraph/man/eQTLnetwork-class.Rd
qpgraph/man/eQTLnetworkEstimate.Rd
qpgraph/man/eQTLnetworkEstimationParam-class.Rd
qpgraph/man/graphParam-class.Rd
qpgraph/man/qpAllCItests.Rd
qpgraph/man/qpAnyGraph.Rd
qpgraph/man/qpAvgNrr.Rd
qpgraph/man/qpBoundary.Rd
qpgraph/man/qpCItest.Rd
qpgraph/man/qpClique.Rd
qpgraph/man/qpCliqueNumber.Rd
qpgraph/man/qpCov.Rd
qpgraph/man/qpEdgeNrr.Rd
qpgraph/man/qpFunctionalCoherence.Rd
qpgraph/man/qpG2Sigma.Rd
qpgraph/man/qpGenNrr.Rd
qpgraph/man/qpGetCliques.Rd
qpgraph/man/qpGraph-class.Rd
qpgraph/man/qpGraphDensity.Rd
qpgraph/man/qpHTF.Rd
qpgraph/man/qpHist.Rd
qpgraph/man/qpIPF.Rd
qpgraph/man/qpImportNrr.Rd
qpgraph/man/qpK2ParCor.Rd
qpgraph/man/qpNrr.Rd
qpgraph/man/qpPAC.Rd
qpgraph/man/qpPCC.Rd
qpgraph/man/qpPRscoreThreshold.Rd
qpgraph/man/qpPathWeight.Rd
qpgraph/man/qpPlotMap.Rd
qpgraph/man/qpPlotNetwork.Rd
qpgraph/man/qpPrecisionRecall.Rd
qpgraph/man/qpRndGraph.Rd
qpgraph/man/qpRndWishart.Rd
qpgraph/man/qpTopPairs.Rd
qpgraph/man/qpUnifRndAssociation.Rd
qpgraph/man/qpUpdateCliquesRemoving.Rd
qpgraph/man/qpgraph-package.Rd
qpgraph/src
qpgraph/src/Makevars.in
qpgraph/src/Makevars.win
qpgraph/src/cliquer.c
qpgraph/src/cliquer.h
qpgraph/src/cliquerconf.h
qpgraph/src/graph.c
qpgraph/src/graph.h
qpgraph/src/misc.h
qpgraph/src/qpgraph.c
qpgraph/src/reorder.c
qpgraph/src/reorder.h
qpgraph/src/set.h
qpgraph/tests
qpgraph/tests/runTests.R
qpgraph/tools
qpgraph/tools/config.guess
qpgraph/tools/config.sub
qpgraph/tools/install-sh
qpgraph/vignettes
qpgraph/vignettes/eQTLnetworks.Rnw
qpgraph/vignettes/qpTxRegNet.Rnw
qpgraph/vignettes/qpgraph.bib
qpgraph/vignettes/qpgraphSimulate.Rnw