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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("qpgraph")
AuthorRobert Castelo [aut, cre], Alberto Roverato [aut]
Bioconductor views GeneExpression GeneRegulation GeneticVariability Genetics GraphAndNetwork Microarray NetworkInference Pathways SNP Software Transcription
Date of publicationNone
MaintainerRobert Castelo <robert.castelo@upf.edu>
LicenseGPL (>= 2)
Version2.10.0
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: Estimation of genetic and molecular regulatory networks from...

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

Functions

addeQTL Man page
addeQTL,eQTLcross-method Man page
addGeneAssociation Man page
addGeneAssociation,eQTLcross-method Man page
addGenes Man page
addGenes,eQTLcross,integer-method Man page
addGenes,eQTLcross,missing-method Man page
addGenes,eQTLcross,numeric-method Man page
alleQTL Man page
alleQTL,eQTLcross-method Man page
alleQTL,eQTLnetwork-method Man page
allGeneAssociations Man page
allGeneAssociations,eQTLnetwork-method Man page
ciseQTL Man page
ciseQTL,eQTLcross,missing-method Man page
ciseQTL,eQTLcross,numeric-method Man page
ciseQTL,eQTLnetwork,missing-method Man page
ciseQTL,eQTLnetwork,numeric-method Man page
determinant,SsdMatrix,logical-method Man page
determinant,SsdMatrix,missing-method Man page
det,SsdMatrix-method Man page
dim,HMgmm-method Man page
dimnames,HMgmm-method Man page
dimnames,SsdMatrix-method Man page
dimnames,UGgmm-method Man page
dim,SsdMatrix-method Man page
dim,UGgmm-method Man page
dRegularGraphParam Man page
dRegularGraphParam-class Man page
dRegularMarkedGraphParam Man page
dRegularMarkedGraphParam-class Man page
EcoliOxygen Man page
eQTLcross Man page
eQTLcross-class Man page
eQTLcross,map,matrix,graphBAM-method Man page
eQTLcross,map,matrix,HMgmm-method Man page
eQTLcross,map,matrix,matrix-method Man page
eQTLcross,map,missing,HMgmm-method Man page
eQTLcross,map,missing,matrix-method Man page
eQTLcross,map,missing,missing-method Man page
$,eQTLcross-method Man page
eQTLcrossParam Man page
eQTLcrossParam-class Man page
eQTLnetwork Man page
eQTLnetwork-class Man page
eQTLnetworkEstimate Man page
eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,eQTLnetwo Man page
eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,missing-m Man page
eQTLnetworkEstimate,eQTLnetworkEstimationParam,missing,eQTLnetwo Man page
eQTLnetworkEstimationParam Man page
eQTLnetworkEstimationParam-class Man page
erGraphParam Man page
erGraphParam-class Man page
erMarkedGraphParam Man page
erMarkedGraphParam-class Man page
filtered.regulon6.1 Man page
gds680.eset Man page
geneAnnotation Man page
geneAnnotation,eQTLnetworkEstimationParam-method Man page
geneAnnotation,eQTLnetwork-method Man page
geneNames Man page
geneNames,eQTLcross-method Man page
geneNames,eQTLnetworkEstimationParam-method Man page
geneNames,eQTLnetwork-method Man page
geneticMap Man page
geneticMap,eQTLnetworkEstimationParam-method Man page
geneticMap,eQTLnetwork-method Man page
ggData Man page
ggData,eQTLnetworkEstimationParam-method Man page
graph Man page
graph,eQTLnetwork-method Man page
graphParam-class Man page
HMgmm Man page
HMgmm-class Man page
HMgmm,graphBAM-method Man page
HMgmm,matrix-method Man page
$,HMgmm-method Man page
HMgmm,missing-method Man page
markedGraphParam-class Man page
markerNames Man page
markerNames,eQTLcross-method Man page
markerNames,eQTLnetworkEstimationParam-method Man page
markerNames,eQTLnetwork-method Man page
names,eQTLcross-method Man page
names,HMgmm-method Man page
names,qpGraph-method Man page
names,UGgmm-method Man page
physicalMap Man page
physicalMap,eQTLnetworkEstimationParam-method Man page
physicalMap,eQTLnetwork-method Man page
plot,eQTLcross,ANY-method Man page
plot,eQTLnetwork,ANY-method Man page
plot,graphBAM,ANY-method Man page
plot,HMgmm,ANY-method Man page
plot,UGgmm,ANY-method Man page
qpAllCItests Man page
qpAllCItests,matrix-method Man page
qpAnyGraph Man page
qpAvgNrr Man page
qpAvgNrr,data.frame-method Man page
qpAvgNrr,ExpressionSet-method Man page
qpAvgNrr,matrix-method Man page
qpBoundary Man page
qpCItest Man page
qpCItest,cross-method Man page
qpCItest,data.frame-method Man page
qpCItest,ExpressionSet-method Man page
qpCItest,matrix-method Man page
qpCItest,SsdMatrix-method Man page
qpClique Man page
qpCliqueNumber Man page
qpCov Man page
qpEdgeCor Man page
qpEdgeCor,matrix-method Man page
qpEdgeCor,UGgmm-method Man page
qpEdgeNrr Man page
qpEdgeNrr,data.frame-method Man page
qpEdgeNrr,ExpressionSet-method Man page
qpEdgeNrr,matrix-method Man page
qpEdgeNrr,SsdMatrix-method Man page
qpFunctionalCoherence Man page
qpFunctionalCoherence,list-method Man page
qpFunctionalCoherence,lsCMatrix-method Man page
qpFunctionalCoherence,lspMatrix-method Man page
qpFunctionalCoherence,lsyMatrix-method Man page
qpFunctionalCoherence,matrix-method Man page
qpG2Sigma Man page
qpGenNrr Man page
qpGenNrr,data.frame-method Man page
qpGenNrr,ExpressionSet-method Man page
qpGenNrr,list-method Man page
qpGenNrr,matrix-method Man page
qpGetCliques Man page
qpgraph Man page
qpGraph Man page
qpGraph-class Man page
qpGraphDensity Man page
qpGraph,dspMatrix-method Man page
qpGraph,matrix-method Man page
$,qpGraph-method Man page
qpgraph-package Man page
qpHist Man page
qpHTF Man page
qpImportNrr Man page
qpIPF Man page
qpK2ParCor Man page
qpNrr Man page
qpNrr,cross-method Man page
qpNrr,data.frame-method Man page
qpNrr,ExpressionSet-method Man page
qpNrr,matrix-method Man page
qpPAC Man page
qpPAC,data.frame-method Man page
qpPAC,ExpressionSet-method Man page
qpPAC,matrix-method Man page
qpPathWeight Man page
qpPathWeight,matrix-method Man page
qpPCC Man page
qpPCC,data.frame-method Man page
qpPCC,ExpressionSet-method Man page
qpPCC,matrix-method Man page
qpPlotMap Man page
qpPlotNetwork Man page
qpPrecisionRecall Man page
qpPRscoreThreshold Man page
qpRndGraph Man page
qpRndWishart Man page
qpTopPairs Man page
qpUnifRndAssociation Man page
qpUpdateCliquesRemoving Man page
rcmvnorm Man page
rcmvnorm,ANY,HMgmm-method Man page
reQTLcross Man page
reQTLcross,eQTLcross,missing-method Man page
reQTLcross,eQTLcrossParam,missing-method Man page
reQTLcross,integer,eQTLcross-method Man page
reQTLcross,integer,eQTLcrossParam-method Man page
reQTLcross,missing,eQTLcross-method Man page
reQTLcross,missing,eQTLcrossParam-method Man page
reQTLcross,numeric,eQTLcross-method Man page
reQTLcross,numeric,eQTLcrossParam-method Man page
resetCutoffs Man page
resetCutoffs,eQTLnetwork-method Man page
rgraphBAM Man page
rgraphBAM,dRegularGraphParam,missing-method Man page
rgraphBAM,erGraphParam,missing-method Man page
rgraphBAM,graphParam,missing-method Man page
rgraphBAM,integer,dRegularGraphParam-method Man page
rgraphBAM,integer,erGraphParam-method Man page
rgraphBAM,integer,graphParam-method Man page
rgraphBAM,missing,dRegularGraphParam-method Man page
rgraphBAM,missing,erGraphParam-method Man page
rgraphBAM,missing,graphParam-method Man page
rgraphBAM,numeric,dRegularGraphParam-method Man page
rgraphBAM,numeric,erGraphParam-method Man page
rgraphBAM,numeric,graphParam-method Man page
rHMgmm Man page
rHMgmm,graphBAM,missing-method Man page
rHMgmm,integer,graphBAM-method Man page
rHMgmm,integer,markedGraphParam-method Man page
rHMgmm,integer,matrix-method Man page
rHMgmm,markedGraphParam,missing-method Man page
rHMgmm,matrix,missing-method Man page
rHMgmm,missing,graphBAM-method Man page
rHMgmm,missing,markedGraphParam-method Man page
rHMgmm,missing,matrix-method Man page
rHMgmm,numeric,graphBAM-method Man page
rHMgmm,numeric,markedGraphParam-method Man page
rHMgmm,numeric,matrix-method Man page
rmvnorm Man page
rmvnorm,integer,numeric-method Man page
rmvnorm,numeric,numeric-method Man page
rmvnorm,numeric,UGgmm-method Man page
rUGgmm Man page
rUGgmm,graphBAM,missing-method Man page
rUGgmm,graphParam,missing-method Man page
rUGgmm,integer,graphBAM-method Man page
rUGgmm,integer,graphParam-method Man page
rUGgmm,integer,matrix-method Man page
rUGgmm,matrix,missing-method Man page
rUGgmm,missing,graphBAM-method Man page
rUGgmm,missing,graphParam-method Man page
rUGgmm,missing,matrix-method Man page
rUGgmm,numeric,graphBAM-method Man page
rUGgmm,numeric,graphParam-method Man page
rUGgmm,numeric,matrix-method Man page
show,eQTLcross-method Man page
show,eQTLcrossParam-method Man page
show,eQTLnetworkEstimationParam-method Man page
show,eQTLnetwork-method Man page
show,graphParam-method Man page
show,HMgmm-method Man page
show,HMgmmSummary-method Man page
show,qpGraph-method Man page
show,SsdMatrix-method Man page
show,UGgmm-method Man page
show,UGgmmSummary-method Man page
sim.cross Man page
sim.cross,map,eQTLcross-method Man page
sim.cross,map,matrix-method Man page
SsdMatrix-class Man page
subset.filtered.regulon6.1 Man page
subset.gds680.eset Man page
summary,HMgmm-method Man page
summary,UGgmm-method Man page
transeQTL Man page
transeQTL,eQTLcross,missing-method Man page
transeQTL,eQTLcross,numeric-method Man page
UGgmm Man page
UGgmm-class Man page
UGgmm,graphBAM-method Man page
UGgmm,matrix-method Man page
$,UGgmm-method Man page
UGgmm,missing-method Man page
varExplained Man page
varExplained,eQTLnetworkEstimationParam,eQTLnetwork-method Man page

Files

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

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