A C D E F G H M N P Q R S T U V misc
qpgraph-package | The q-order partial correlation graph learning software, qpgraph. |
addeQTL | eQTL experimental cross model class |
addeQTL-method | eQTL experimental cross model class |
addGeneAssociation | eQTL experimental cross model class |
addGeneAssociation-method | eQTL experimental cross model class |
addGenes | eQTL experimental cross model class |
addGenes-method | eQTL experimental cross model class |
alleQTL | eQTL network model class |
alleQTL-method | eQTL experimental cross model class |
alleQTL-method | eQTL network model class |
allGeneAssociations | eQTL network model class |
allGeneAssociations-method | eQTL network model class |
ciseQTL | eQTL network model class |
ciseQTL-method | eQTL experimental cross model class |
ciseQTL-method | eQTL network model class |
det-method | Sum of squares and deviations Matrices |
determinant-method | Sum of squares and deviations Matrices |
dim-method | Homogeneous mixed graphical Markov model |
dim-method | Sum of squares and deviations Matrices |
dim-method | Undirected Gaussian graphical Markov model |
dimnames-method | Homogeneous mixed graphical Markov model |
dimnames-method | Sum of squares and deviations Matrices |
dimnames-method | Undirected Gaussian graphical Markov model |
dRegularGraphParam | Graph parameter classes |
dRegularGraphParam-class | Graph parameter classes |
dRegularMarkedGraphParam | Graph parameter classes |
dRegularMarkedGraphParam-class | Graph parameter classes |
EcoliOxygen | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
eQTLcross | eQTL experimental cross model class |
eQTLcross-class | eQTL experimental cross model class |
eQTLcross-method | eQTL experimental cross model class |
eQTLcrossParam | eQTL experimental cross model class |
eQTLcrossParam-class | eQTL experimental cross model class |
eQTLnetwork | eQTL network model class |
eQTLnetwork-class | eQTL network model class |
eQTLnetworkEstimate | Estimation of a eQTL network from genetical genomics data |
eQTLnetworkEstimate-method | Estimation of a eQTL network from genetical genomics data |
eQTLnetworkEstimationParam | eQTL network parameter model class |
eQTLnetworkEstimationParam-class | eQTL network parameter model class |
erGraphParam | Graph parameter classes |
erGraphParam-class | Graph parameter classes |
erMarkedGraphParam | Graph parameter classes |
erMarkedGraphParam-class | Graph parameter classes |
filtered.regulon6.1 | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
gds680.eset | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
geneAnnotation | eQTL network parameter model class |
geneAnnotation-method | eQTL network model class |
geneAnnotation-method | eQTL network parameter model class |
geneNames | eQTL network parameter model class |
geneNames-method | eQTL experimental cross model class |
geneNames-method | eQTL network model class |
geneNames-method | eQTL network parameter model class |
geneticMap | eQTL network parameter model class |
geneticMap-method | eQTL network model class |
geneticMap-method | eQTL network parameter model class |
ggData | eQTL network parameter model class |
ggData-method | eQTL network parameter model class |
graph | eQTL network model class |
graph-method | eQTL network model class |
graphParam-class | Graph parameter classes |
HMgmm | Homogeneous mixed graphical Markov model |
HMgmm-class | Homogeneous mixed graphical Markov model |
HMgmm-method | Homogeneous mixed graphical Markov model |
markedGraphParam-class | Graph parameter classes |
markerNames | eQTL network parameter model class |
markerNames-method | eQTL experimental cross model class |
markerNames-method | eQTL network model class |
markerNames-method | eQTL network parameter model class |
names-method | Homogeneous mixed graphical Markov model |
names-method | Undirected Gaussian graphical Markov model |
names-method | eQTL experimental cross model class |
physicalMap | eQTL network parameter model class |
physicalMap-method | eQTL network model class |
physicalMap-method | eQTL network parameter model class |
plot-method | Homogeneous mixed graphical Markov model |
plot-method | Undirected Gaussian graphical Markov model |
plot-method | eQTL experimental cross model class |
plot-method | eQTL network model class |
plot-method | Graph parameter classes |
qpAllCItests | Tests of conditional independence |
qpAllCItests-method | Tests of conditional independence |
qpAnyGraph | A graph |
qpAvgNrr | Average non-rejection rate estimation |
qpAvgNrr-method | Average non-rejection rate estimation |
qpBoundary | Maximum boundary size of the resulting qp-graphs |
qpCItest | Conditional independence test |
qpCItest-method | Conditional independence test |
qpClique | Complexity of the resulting qp-graphs |
qpCliqueNumber | Clique number |
qpCov | Calculation of the sample covariance matrix |
qpEdgeCor | Non-rejection rate estimation for a pair of variables |
qpEdgeCor-method | Non-rejection rate estimation for a pair of variables |
qpEdgeNrr | Non-rejection rate estimation for a pair of variables |
qpEdgeNrr-method | Non-rejection rate estimation for a pair of variables |
qpFunctionalCoherence | Functional coherence estimation |
qpFunctionalCoherence-method | Functional coherence estimation |
qpG2Sigma | Random covariance matrix |
qpGenNrr | Generalized non-rejection rate estimation |
qpGenNrr-method | Generalized non-rejection rate estimation |
qpGetCliques | Clique list |
qpGraph | The qp-graph |
qpgraph | The q-order partial correlation graph learning software, qpgraph. |
qpGraph-class | The qp-graph |
qpGraph-method | The qp-graph |
qpGraphDensity | Densities of resulting qp-graphs |
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 |
qpNrr-method | Non-rejection rate estimation |
qpPAC | Estimation of partial correlation coefficients |
qpPAC-method | Estimation of partial correlation coefficients |
qpPCC | Estimation of Pearson correlation coefficients |
qpPCC-method | 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 or recall levels |
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 |
rcmvnorm | Homogeneous mixed graphical Markov model |
rcmvnorm-method | Homogeneous mixed graphical Markov model |
reQTLcross | eQTL experimental cross model class |
reQTLcross-method | eQTL experimental cross model class |
resetCutoffs | eQTL network model class |
resetCutoffs-method | eQTL network model class |
rgraphBAM | Graph parameter classes |
rgraphBAM-method | Graph parameter classes |
rHMgmm | Homogeneous mixed graphical Markov model |
rHMgmm-method | Homogeneous mixed graphical Markov model |
rmvnorm | Undirected Gaussian graphical Markov model |
rmvnorm-method | Undirected Gaussian graphical Markov model |
rUGgmm | Undirected Gaussian graphical Markov model |
rUGgmm-method | Undirected Gaussian graphical Markov model |
show-method | Homogeneous mixed graphical Markov model |
show-method | Sum of squares and deviations Matrices |
show-method | Undirected Gaussian graphical Markov model |
show-method | eQTL experimental cross model class |
show-method | eQTL network model class |
show-method | eQTL network parameter model class |
show-method | Graph parameter classes |
show-method | The qp-graph |
sim.cross | eQTL experimental cross model class |
sim.cross-method | eQTL experimental cross model class |
SsdMatrix-class | Sum of squares and deviations Matrices |
subset.filtered.regulon6.1 | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
subset.gds680.eset | Preprocessed microarray oxygen deprivation data and filtered RegulonDB data |
summary-method | Homogeneous mixed graphical Markov model |
summary-method | Undirected Gaussian graphical Markov model |
transeQTL | eQTL experimental cross model class |
transeQTL-method | eQTL experimental cross model class |
UGgmm | Undirected Gaussian graphical Markov model |
UGgmm-class | Undirected Gaussian graphical Markov model |
UGgmm-method | Undirected Gaussian graphical Markov model |
varExplained | eQTL network model class |
varExplained-method | eQTL network model class |
$-method | Homogeneous mixed graphical Markov model |
$-method | Undirected Gaussian graphical Markov model |
$-method | eQTL experimental cross model class |