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

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Search the rcastelo/qpgraph package
Vignettes
Functions
355
Source code
25
Man pages
44
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rcastelo/qpgraph: Estimation of genetic and molecular regulatory networks from high-throughput genomics data
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API

API for rcastelo/qpgraph
Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Global functions
$,HMgmm-method Man page
$,UGgmm-method Man page
$,eQTLcross-method Man page
$,qpGraph-method Man page
.calculateCondMean Source code
.eQTLplotHive Source code
.expandTerms Source code
.i2e Source code
.isPkgLoaded Source code
.old_qpGraph Source code
.onLoad Source code
.parseFormula Source code
.ploteQTLnetworkHive Source code
.processParameters Source code
.qpAllCItests Source code
.qpAvgNrr Source code
.qpCItest Source code
.qpCItestHMGM Source code
.qpCliqueNumberLowerBound Source code
.qpCliqueNumberOstergard Source code
.qpEdgeNrr Source code
.qpEdgeNrrHMGM Source code
.qpEdgeNrrIdenticalQs Source code
.qpEdgePACSE Source code
.qpFastAllCItests Source code
.qpFastAllCItestsPar Source code
.qpFastCItestHMGM Source code
.qpFastCItestOpt Source code
.qpFastCItestStd Source code
.qpFastCliquerGetCliques Source code
.qpFastEdgeNrr Source code
.qpFastEdgeNrrHMGM Source code
.qpFastHTF Source code
.qpFastIPF Source code
.qpFastNrr Source code
.qpFastNrrIdenticalQs Source code
.qpFastNrrIdenticalQsPar Source code
.qpFastNrrPar Source code
.qpFastPACSE Source code
.qpFastRndGraph Source code
.qpFastUpdateCliquesRemoving Source code
.qpFilterByGO Source code
.qpFunctionalCoherence Source code
.qpGenNrr Source code
.qpGraph Source code
.qpIPFpass Source code
.qpIPFstep Source code
.qpIsPackageInstalled Source code
.qpIsPackageLoaded Source code
.qpNrr Source code
.qpNrrIdenticalQs Source code
.qpPAC Source code
.qpPCC Source code
.qpRndRegularGraph Source code
.replaceFormulaQs Source code
.ssdStatsCompleteObs Source code
.ssdStatsEM Source code
EcoliOxygen Man page
GOenv Source code
HMgmm Man page
HMgmm,graphBAM-method Man page
HMgmm,matrix-method Man page
HMgmm,missing-method Man page
HMgmm-class Man page
Ki Source code
SsdMatrix-class Man page
UGgmm Man page
UGgmm,graphBAM-method Man page
UGgmm,matrix-method Man page
UGgmm,missing-method Man page
UGgmm-class 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
addeQTL Man page
addeQTL,eQTLcross-method Man page
allGeneAssociations Man page
allGeneAssociations,eQTLnetwork-method Man page
alleQTL Man page
alleQTL,eQTLcross-method Man page
alleQTL,eQTLnetwork-method Man page
calculateEta2 Source code
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
clPrCall Source code
convergence Source code
dRegularGraphParam Man page Source code
dRegularGraphParam-class Man page
dRegularMarkedGraphParam Man page Source code
dRegularMarkedGraphParam-class Man page
det,SsdMatrix-method Man page
determinant,SsdMatrix,logical-method Man page
determinant,SsdMatrix,missing-method Man page
dim,HMgmm-method Man page
dim,SsdMatrix-method Man page
dim,UGgmm-method Man page
dimnames,HMgmm-method Man page
dimnames,SsdMatrix-method Man page
dimnames,UGgmm-method Man page
eQTLcross Man page
eQTLcross,map,matrix,HMgmm-method Man page
eQTLcross,map,matrix,graphBAM-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-class Man page
eQTLcrossParam Man page Source code
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 Source code
eQTLnetworkEstimationParam-class Man page
erGraphParam Man page Source code
erGraphParam-class Man page
erMarkedGraphParam Man page Source code
erMarkedGraphParam-class Man page
filterCollinearities Man page Source code
filtered.regulon6.1 Man page
gds680.eset Man page
geneAnnotation Man page
geneAnnotation,eQTLnetwork-method Man page
geneAnnotation,eQTLnetworkEstimationParam-method Man page
geneNames Man page
geneNames,eQTLcross-method Man page
geneNames,eQTLnetwork-method Man page
geneNames,eQTLnetworkEstimationParam-method Man page
geneticMap Man page
geneticMap,eQTLnetwork-method Man page
geneticMap,eQTLnetworkEstimationParam-method Man page
ggData Man page
ggData,eQTLnetworkEstimationParam-method Man page
graph Man page
graph,eQTLnetwork-method Man page
graphParam-class Man page
markedGraphParam-class Man page
markerNames Man page
markerNames,eQTLcross-method Man page
markerNames,eQTLnetwork-method Man page
markerNames,eQTLnetworkEstimationParam-method Man page
names,HMgmm-method Man page
names,UGgmm-method Man page
names,eQTLcross-method Man page
names,qpGraph-method Man page
physicalMap Man page
physicalMap,eQTLnetwork-method Man page
physicalMap,eQTLnetworkEstimationParam-method Man page
plot,HMgmm,ANY-method Man page
plot,UGgmm,ANY-method Man page
plot,eQTLcross,ANY-method Man page
plot,eQTLnetwork,ANY-method Man page
plot,graphBAM,ANY-method Man page
prob_i Source code
qPretty Source code
qpAllCItests Man page
qpAllCItests,matrix-method Man page
qpAnyGraph Man page Source code
qpAvgNrr Man page
qpAvgNrr,ExpressionSet-method Man page
qpAvgNrr,data.frame-method Man page
qpAvgNrr,matrix-method Man page
qpBoundary Man page Source code
qpCItest Man page
qpCItest,ExpressionSet-method Man page
qpCItest,SsdMatrix-method Man page
qpCItest,cross-method Man page
qpCItest,data.frame-method Man page
qpCItest,matrix-method Man page
qpClique Man page Source code
qpCliqueNumber Man page Source code
qpCov Man page Source code
qpEdgeCor Man page
qpEdgeCor,UGgmm-method Man page
qpEdgeCor,matrix-method Man page
qpEdgeNrr Man page
qpEdgeNrr,ExpressionSet-method Man page
qpEdgeNrr,SsdMatrix-method Man page
qpEdgeNrr,data.frame-method Man page
qpEdgeNrr,matrix-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,ExpressionSet-method Man page
qpGenNrr,data.frame-method Man page
qpGenNrr,list-method Man page
qpGenNrr,matrix-method Man page
qpGetCliques Man page Source code
qpGraph Man page
qpGraph,dspMatrix-method Man page
qpGraph,matrix-method Man page
qpGraph-class Man page
qpGraphDensity Man page Source code
qpHTF Man page Source code
qpHist Man page Source code
qpIPF Man page Source code
qpImportNrr Man page Source code
qpK2ParCor Man page Source code
qpNrr Man page
qpNrr,ExpressionSet-method Man page
qpNrr,cross-method Man page
qpNrr,data.frame-method Man page
qpNrr,matrix-method Man page
qpPAC Man page
qpPAC,ExpressionSet-method Man page
qpPAC,data.frame-method Man page
qpPAC,matrix-method Man page
qpPCC Man page
qpPCC,ExpressionSet-method Man page
qpPCC,data.frame-method Man page
qpPCC,matrix-method Man page
qpPRscoreThreshold Man page Source code
qpPathWeight Man page
qpPathWeight,dspMatrix-method Man page
qpPathWeight,matrix-method Man page
qpPlotMap Man page Source code
qpPlotNetwork Man page Source code
qpPrecisionRecall Man page Source code
qpRndGraph Man page Source code
qpRndWishart Man page Source code
qpTopPairs Man page Source code
qpUnifRndAssociation Man page
qpUpdateCliquesRemoving Man page Source code
qpgraph Man page
qpgraph-package 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
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
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
rmvnorm Man page Source code
rmvnorm,integer,numeric-method Man page
rmvnorm,numeric,UGgmm-method Man page
rmvnorm,numeric,numeric-method Man page
rmvnorm.UGgmm Source code
rmvnorm.default Source code
rmvnorm.numeric Source code
show,HMgmm-method Man page
show,HMgmmSummary-method Man page
show,SsdMatrix-method Man page
show,UGgmm-method Man page
show,UGgmmSummary-method Man page
show,eQTLcross-method Man page
show,eQTLcrossParam-method Man page
show,eQTLnetwork-method Man page
show,eQTLnetworkEstimationParam-method Man page
show,graphParam-method Man page
show,qpGraph-method Man page
sim.cross Man page Source code
sim.cross,map,eQTLcross-method Man page
sim.cross,map,matrix-method Man page
sim.cross.default Source code
sim.cross.eQTLcross Source code
sim.cross.matrix Source code
stat_com Source code
stat_mis Source code
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
varExplained Man page
varExplained,eQTLnetworkEstimationParam,eQTLnetwork-method Man page
rcastelo/qpgraph documentation built on Oct. 28, 2024, 5:15 a.m.

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