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qpgraph (version 2.6.1)

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

Description

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

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Version

Version

2.6.1

License

GPL (>= 2)

Maintainer

Robert Castelo

Last Published

February 15th, 2017

Functions in qpgraph (2.6.1)

qpAllCItests

Tests of conditional independence
eQTLnetworkEstimationParam-class

eQTL network parameter model class
qpClique

Complexity of the resulting qp-graphs
qpEdgeNrr

Non-rejection rate estimation for a pair of variables
qpPCC

Estimation of Pearson correlation coefficients
qpHTF

Hastie Tibshirani Friedman iterative regression algorithm
qpImportNrr

Import non-rejection rates
qpAnyGraph

A graph
qpUnifRndAssociation

Uniformly random association values
qpAvgNrr

Average non-rejection rate estimation
SsdMatrix-class

Sum of squares and deviations Matrices
qpG2Sigma

Random covariance matrix
UGgmm-class

Undirected Gaussian graphical Markov model
qpCov

Calculation of the sample covariance matrix
qpCliqueNumber

Clique number
qpgraph-package

The q-order partial correlation graph learning software, qpgraph.
qpTopPairs

Report pairs of variables
qpIPF

Iterative proportional fitting algorithm
qpPAC

Estimation of partial correlation coefficients
qpPlotNetwork

Plots a graph
qpGenNrr

Generalized non-rejection rate estimation
qpCItest

Conditional independence test
qpNrr

Non-rejection rate estimation
eQTLnetworkEstimate

Estimation of a eQTL network from genetical genomics data
qpPrecisionRecall

Calculation of precision-recall curves
qpGraph-class

The qp-graph
qpRndWishart

Random Wishart distribution
qpUpdateCliquesRemoving

Update clique list when removing one edge
qpBoundary

Maximum boundary size of the resulting qp-graphs
qpPathWeight

Calculation of path weights
qpRndGraph

Undirected random d-regular graphs
graphParam-class

Graph parameter classes
eQTLcross-class

eQTL experimental cross model class
HMgmm-class

Homogeneous mixed graphical Markov model
qpHist

Histograms of non-rejection rates
qpK2ParCor

Partial correlation coefficients
EcoliOxygen

Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
eQTLnetwork-class

eQTL network model class
qpGraphDensity

Densities of resulting qp-graphs
qpFunctionalCoherence

Functional coherence estimation
qpPlotMap

Plots a map of associated pairs
qpPRscoreThreshold

Calculation of scores thresholds attaining nominal precision or recall levels
qpGetCliques

Clique list