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