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 | 2.8.2 |

http://functionalgenomics.upf.edu/qpgraph |

**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

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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