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.

AuthorRobert Castelo [aut, cre], Alberto Roverato [aut]
Date of publicationNone
MaintainerRobert Castelo <robert.castelo@upf.edu>
LicenseGPL (>= 2)
Version2.8.2
http://functionalgenomics.upf.edu/qpgraph

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

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