Package: qpgraph 2.39.0

Robert Castelo

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.

Authors:Robert Castelo [aut, cre], Alberto Roverato [aut]

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NEWS

# Install 'qpgraph' in R:

install.packages('qpgraph', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rcastelo/rcastelo/issues

Uses libs:

openblas– Optimized BLAS

Datasets:

filtered.regulon6.1 - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
gds680.eset - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
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

On BioConductor:qpgraph-2.39.0(bioc 3.20)qpgraph-2.38.0(bioc 3.19)

bioconductor-package

73 exports 1.58 score 74 dependencies 2 dependents 9 mentions

Last updated 2 months agofrom:9740db95e5

Exports:addeQTL addGeneAssociation addGenes alleQTL allGeneAssociations ciseQTL det determinant dRegularGraphParam dRegularMarkedGraphParam eQTLcross eQTLcrossParam eQTLnetworkEstimate eQTLnetworkEstimationParam erGraphParam erMarkedGraphParam filterCollinearities geneAnnotation geneNames geneticMap ggData graph HMgmm markerNames physicalMap plot qpAllCItests qpAnyGraph qpAvgNrr qpBoundary qpCItest qpClique qpCliqueNumber qpCov qpEdgeCor qpEdgeNrr qpFunctionalCoherence qpG2Sigma qpGenNrr qpGetCliques qpGraph qpGraphDensity qpHist qpHTF qpImportNrr qpIPF qpK2ParCor qpNrr qpPAC qpPathWeight qpPCC qpPlotMap qpPlotNetwork qpPrecisionRecall qpPRscoreThreshold qpRndGraph qpRndWishart qpTopPairs qpUnifRndAssociation qpUpdateCliquesRemoving rcmvnorm reQTLcross resetCutoffs rgraphBAM rHMgmm rmvnorm rUGgmm show sim.cross summary transeQTL UGgmm varExplained

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue graph httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime mvtnorm openssl pkgconfig plogr png qtl R6 RCurl restfulr Rgraphviz Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils vctrs XML xtable XVector yaml zlibbioc

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Estimation of genetic and molecular regulatory networks from high-throughput genomics data	qpgraph-package qpgraph
Preprocessed microarray oxygen deprivation data and filtered RegulonDB data	EcoliOxygen filtered.regulon6.1 gds680.eset subset.filtered.regulon6.1 subset.gds680.eset
eQTL experimental cross model class	$,eQTLcross-method addeQTL addeQTL,eQTLcross-method addGeneAssociation addGeneAssociation,eQTLcross-method addGenes addGenes,eQTLcross,integer-method addGenes,eQTLcross,missing-method addGenes,eQTLcross,numeric-method alleQTL,eQTLcross-method ciseQTL,eQTLcross,missing-method ciseQTL,eQTLcross,numeric-method eQTLcross eQTLcross,map,matrix,graphBAM-method eQTLcross,map,matrix,HMgmm-method eQTLcross,map,matrix,matrix-method eQTLcross,map,missing,HMgmm-method eQTLcross,map,missing,matrix-method eQTLcross,map,missing,missing-method eQTLcross-class eQTLcrossParam eQTLcrossParam-class geneNames,eQTLcross-method markerNames,eQTLcross-method names,eQTLcross-method plot,eQTLcross,ANY-method reQTLcross reQTLcross,eQTLcross,missing-method reQTLcross,eQTLcrossParam,missing-method reQTLcross,integer,eQTLcross-method reQTLcross,integer,eQTLcrossParam-method reQTLcross,missing,eQTLcross-method reQTLcross,missing,eQTLcrossParam-method reQTLcross,numeric,eQTLcross-method reQTLcross,numeric,eQTLcrossParam-method show,eQTLcross-method show,eQTLcrossParam-method sim.cross sim.cross,map,eQTLcross-method sim.cross,map,matrix-method transeQTL transeQTL,eQTLcross,missing-method transeQTL,eQTLcross,numeric-method
eQTL network model class	alleQTL alleQTL,eQTLnetwork-method allGeneAssociations allGeneAssociations,eQTLnetwork-method ciseQTL ciseQTL,eQTLnetwork,missing-method ciseQTL,eQTLnetwork,numeric-method eQTLnetwork eQTLnetwork-class geneAnnotation,eQTLnetwork-method geneNames,eQTLnetwork-method geneticMap,eQTLnetwork-method graph graph,eQTLnetwork-method markerNames,eQTLnetwork-method physicalMap,eQTLnetwork-method plot,eQTLnetwork,ANY-method resetCutoffs resetCutoffs,eQTLnetwork-method show,eQTLnetwork-method varExplained varExplained,eQTLnetworkEstimationParam,eQTLnetwork-method
Estimation of a eQTL network from genetical genomics data	eQTLnetworkEstimate eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,eQTLnetwork-method eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,missing-method eQTLnetworkEstimate,eQTLnetworkEstimationParam,missing,eQTLnetwork-method
eQTL network parameter model class	eQTLnetworkEstimationParam eQTLnetworkEstimationParam-class geneAnnotation geneAnnotation,eQTLnetworkEstimationParam-method geneNames geneNames,eQTLnetworkEstimationParam-method geneticMap geneticMap,eQTLnetworkEstimationParam-method ggData ggData,eQTLnetworkEstimationParam-method markerNames markerNames,eQTLnetworkEstimationParam-method physicalMap physicalMap,eQTLnetworkEstimationParam-method show,eQTLnetworkEstimationParam-method
Filter collinearities	filterCollinearities
Graph parameter classes	dRegularGraphParam dRegularGraphParam-class dRegularMarkedGraphParam dRegularMarkedGraphParam-class erGraphParam erGraphParam-class erMarkedGraphParam erMarkedGraphParam-class graphParam-class markedGraphParam-class plot,graphBAM,ANY-method rgraphBAM rgraphBAM,dRegularGraphParam,missing-method rgraphBAM,erGraphParam,missing-method rgraphBAM,graphParam,missing-method rgraphBAM,integer,dRegularGraphParam-method rgraphBAM,integer,erGraphParam-method rgraphBAM,integer,graphParam-method rgraphBAM,missing,dRegularGraphParam-method rgraphBAM,missing,erGraphParam-method rgraphBAM,missing,graphParam-method rgraphBAM,numeric,dRegularGraphParam-method rgraphBAM,numeric,erGraphParam-method rgraphBAM,numeric,graphParam-method show,graphParam-method
Homogeneous mixed graphical Markov model	$,HMgmm-method dim,HMgmm-method dimnames,HMgmm-method HMgmm HMgmm,graphBAM-method HMgmm,matrix-method HMgmm,missing-method HMgmm-class names,HMgmm-method plot,HMgmm,ANY-method rcmvnorm rcmvnorm,ANY,HMgmm-method rHMgmm rHMgmm,graphBAM,missing-method rHMgmm,integer,graphBAM-method rHMgmm,integer,markedGraphParam-method rHMgmm,integer,matrix-method rHMgmm,markedGraphParam,missing-method rHMgmm,matrix,missing-method rHMgmm,missing,graphBAM-method rHMgmm,missing,markedGraphParam-method rHMgmm,missing,matrix-method rHMgmm,numeric,graphBAM-method rHMgmm,numeric,markedGraphParam-method rHMgmm,numeric,matrix-method show,HMgmm-method show,HMgmmSummary-method summary,HMgmm-method
Tests of conditional independence	qpAllCItests qpAllCItests,matrix-method
A graph	qpAnyGraph
Average non-rejection rate estimation	qpAvgNrr qpAvgNrr,data.frame-method qpAvgNrr,ExpressionSet-method qpAvgNrr,matrix-method
Maximum boundary size of the resulting qp-graphs	qpBoundary
Conditional independence test	qpCItest qpCItest,cross-method qpCItest,data.frame-method qpCItest,ExpressionSet-method qpCItest,matrix-method qpCItest,SsdMatrix-method
Complexity of the resulting qp-graphs	qpClique
Clique number	qpCliqueNumber
Calculation of the sample covariance matrix	qpCov
Non-rejection rate estimation for a pair of variables	qpEdgeCor qpEdgeCor,matrix-method qpEdgeCor,UGgmm-method qpEdgeNrr qpEdgeNrr,data.frame-method qpEdgeNrr,ExpressionSet-method qpEdgeNrr,matrix-method qpEdgeNrr,SsdMatrix-method
Functional coherence estimation	qpFunctionalCoherence qpFunctionalCoherence,list-method qpFunctionalCoherence,lsCMatrix-method qpFunctionalCoherence,lspMatrix-method qpFunctionalCoherence,lsyMatrix-method qpFunctionalCoherence,matrix-method
Random covariance matrix	qpG2Sigma
Generalized non-rejection rate estimation	qpGenNrr qpGenNrr,data.frame-method qpGenNrr,ExpressionSet-method qpGenNrr,list-method qpGenNrr,matrix-method
Clique list	qpGetCliques
The qp-graph	$,qpGraph-method names,qpGraph-method qpGraph qpGraph,dspMatrix-method qpGraph,matrix-method qpGraph-class show,qpGraph-method
Densities of resulting qp-graphs	qpGraphDensity
Histograms of non-rejection rates	qpHist
Hastie Tibshirani Friedman iterative regression algorithm	qpHTF
Import non-rejection rates	qpImportNrr
Iterative proportional fitting algorithm	qpIPF
Partial correlation coefficients	qpK2ParCor
Non-rejection rate estimation	qpNrr qpNrr,cross-method qpNrr,data.frame-method qpNrr,ExpressionSet-method qpNrr,matrix-method
Estimation of partial correlation coefficients	qpPAC qpPAC,data.frame-method qpPAC,ExpressionSet-method qpPAC,matrix-method
Calculation of path weights	qpPathWeight qpPathWeight,dspMatrix-method qpPathWeight,matrix-method
Estimation of Pearson correlation coefficients	qpPCC qpPCC,data.frame-method qpPCC,ExpressionSet-method qpPCC,matrix-method
Plots a map of associated pairs	qpPlotMap
Plots a graph	qpPlotNetwork
Calculation of precision-recall curves	qpPrecisionRecall
Calculation of scores thresholds attaining nominal precision or recall levels	qpPRscoreThreshold
Undirected random d-regular graphs	qpRndGraph
Random Wishart distribution	qpRndWishart
Report pairs of variables	qpTopPairs
Uniformly random association values	qpUnifRndAssociation
Update clique list when removing one edge	qpUpdateCliquesRemoving
Sum of squares and deviations Matrices	det,SsdMatrix-method determinant,SsdMatrix,logical-method determinant,SsdMatrix,missing-method dim,SsdMatrix-method dimnames,SsdMatrix-method show,SsdMatrix-method SsdMatrix-class
Undirected Gaussian graphical Markov model	$,UGgmm-method dim,UGgmm-method dimnames,UGgmm-method names,UGgmm-method plot,UGgmm,ANY-method rmvnorm rmvnorm,integer,numeric-method rmvnorm,numeric,numeric-method rmvnorm,numeric,UGgmm-method rUGgmm rUGgmm,graphBAM,missing-method rUGgmm,graphParam,missing-method rUGgmm,integer,graphBAM-method rUGgmm,integer,graphParam-method rUGgmm,integer,matrix-method rUGgmm,matrix,missing-method rUGgmm,missing,graphBAM-method rUGgmm,missing,graphParam-method rUGgmm,missing,matrix-method rUGgmm,numeric,graphBAM-method rUGgmm,numeric,graphParam-method rUGgmm,numeric,matrix-method show,UGgmm-method show,UGgmmSummary-method summary,UGgmm-method UGgmm UGgmm,graphBAM-method UGgmm,matrix-method UGgmm,missing-method UGgmm-class