rJPSGCS: R-interface to Gene Drop Simulation from JPSGCS
Version 0.2-7

R-interface to gene drop programs from Alun Thomas' Java Programs for Statistical Genetics and Computational Statistics (JPSGCS)

AuthorSigal Blay [aut], Jinko Graham [aut], Brad McNeney [aut, cre], Annick Nembot-Simo [aut], Alun Thomas [ctb], Hin-Tak Leung [ctb]
Date of publication2014-12-08 09:54:39
MaintainerBrad McNeney <mcneney@sfu.ca>
LicenseGPL-3
Version0.2-7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rJPSGCS")

Getting started

Package overview

Popular man pages

exdat: example data for rJPSGCS
FitGMLD: estimate a graphical model for linkage disequilibrium
GeneDrops: simulate genotypes on a pedigree
read.pedfile: read a LINKAGE pedigree file into a 'snp.matrix' object
rJPSGCS-package: R wrappers for JPSGCS gene drop programs.
write.parfile: write a LINKAGE parameter file
write.pedfile: write a 'snp.matrix' object to a LINKAGE pedigree file.
See all...

All man pages Function index File listing

Man pages

exdat: example data for rJPSGCS
FitGMLD: estimate a graphical model for linkage disequilibrium
GeneDrops: simulate genotypes on a pedigree
read.pedfile: read a LINKAGE pedigree file into a 'snp.matrix' object
rJPSGCS-package: R wrappers for JPSGCS gene drop programs.
write.parfile: write a LINKAGE parameter file
write.pedfile: write a 'snp.matrix' object to a LINKAGE pedigree file.

Functions

FitGMLD Man page Source code
GeneDrops Man page Source code
ast.lib Source code
exdat Man page
make.unrel.pedinf Source code
onLoad Source code
rJPSGCS Man page
rJPSGCS-package Man page
read.pedfile Man page Source code
read.pedfile.info Source code
read.pedfile.map Source code
write.parfile Man page Source code
write.pedfile Man page Source code

Files

inst
inst/NEWS
inst/java
inst/java/JPSGCS.jar
src
src/Makevars
src/read_pedfile_priv.h
src/readPEDfile.c
src/Makevars.win
src/writePEDfile.c
src/writeTrasposedPEDfile.c
NAMESPACE
data
data/exdat.rda
R
R/read.pedfile.R
R/write.pedfile.R
R/FitGMLD.R
R/write.parfile.R
R/zzz.R
R/GeneDrops.R
MD5
java
java/CheckParameters.java
java/HomozygousSGS.java
java/HetCutOff.java
java/McLinkage.java
java/McTLods.java
java/McKinship.java
java/COPYING
java/SimSGS.java
java/GCHap.java
java/GetPolymorphisms.java
java/GeneDrop.java
java/CheckErrors.java
java/package.html
java/SimHomozygousSGS.java
java/DownCodeAlleles.java
java/SimHGS.java
java/Complete.java
java/LinkageToFastPhase.java
java/LDModelToGraph.java
java/ViewLinkPed.java
java/FitGMLDNoWind.java
java/ZeroLoopPed.java
java/SelectLoci.java
java/jpsgcs
java/jpsgcs/alun
java/jpsgcs/alun/pedmcmc
java/jpsgcs/alun/pedmcmc/ExtendedLMSampler.java
java/jpsgcs/alun/pedmcmc/Inheritance.java
java/jpsgcs/alun/pedmcmc/GenepiFunction.java
java/jpsgcs/alun/pedmcmc/LDModel.java
java/jpsgcs/alun/pedmcmc/AuxLocusFunction.java
java/jpsgcs/alun/pedmcmc/Allele.java
java/jpsgcs/alun/pedmcmc/TwoLocusProduct.java
java/jpsgcs/alun/pedmcmc/TwoSidedRecombination.java
java/jpsgcs/alun/pedmcmc/ErrorLocusProduct.java
java/jpsgcs/alun/pedmcmc/AuxOneGenVariable.java
java/jpsgcs/alun/pedmcmc/LocusSampler.java
java/jpsgcs/alun/pedmcmc/GenotypeErrorPenetrance.java
java/jpsgcs/alun/pedmcmc/AllelePenetrance.java
java/jpsgcs/alun/pedmcmc/AlleleTransmission.java
java/jpsgcs/alun/pedmcmc/AuxVariable.java
java/jpsgcs/alun/pedmcmc/LocusProduct.java
java/jpsgcs/alun/pedmcmc/AuxGraphicalModel.java
java/jpsgcs/alun/pedmcmc/Recombination.java
java/jpsgcs/alun/pedmcmc/AlleleErrorPenetrance.java
java/jpsgcs/alun/pedmcmc/ErrorPrior.java
java/jpsgcs/alun/pedmcmc/AlleleSegregation.java
java/jpsgcs/alun/pedmcmc/Genotype.java
java/jpsgcs/alun/pedmcmc/GenotypePrior.java
java/jpsgcs/alun/pedmcmc/AllelePrior.java
java/jpsgcs/alun/pedmcmc/GenotypePenetrance.java
java/jpsgcs/alun/pedmcmc/AuxThreeGenVariable.java
java/jpsgcs/alun/pedmcmc/AuxLinkFunction.java
java/jpsgcs/alun/pedmcmc/LocusMeiosisSampler.java
java/jpsgcs/alun/pedmcmc/Error.java
java/jpsgcs/alun/zeroloop
java/jpsgcs/alun/zeroloop/TwoParentConstraint.java
java/jpsgcs/alun/zeroloop/ZeroLoopPedGenerator.java
java/jpsgcs/alun/zeroloop/MonogamyConstraint.java
java/jpsgcs/alun/zeroloop/EdgeConstraint.java
java/jpsgcs/alun/zeroloop/RandomPedTree.java
java/jpsgcs/alun/zeroloop/Edge.java
java/jpsgcs/alun/zeroloop/OneParentalMarriageConstraint.java
java/jpsgcs/alun/zeroloop/Marriage.java
java/jpsgcs/alun/zeroloop/PedNode.java
java/jpsgcs/alun/zeroloop/Individual.java
java/jpsgcs/alun/random
java/jpsgcs/alun/random/WichmanHill.java
java/jpsgcs/alun/random/GammaRV.java
java/jpsgcs/alun/random/Random.java
java/jpsgcs/alun/random/StochasticProcess.java
java/jpsgcs/alun/random/WeibullRV.java
java/jpsgcs/alun/random/AhrensDieter.java
java/jpsgcs/alun/random/BrownianMotion.java
java/jpsgcs/alun/random/Sampler.java
java/jpsgcs/alun/random/RandomUrn.java
java/jpsgcs/alun/random/IntSampling.java
java/jpsgcs/alun/random/IntWithoutReplacement.java
java/jpsgcs/alun/random/StochasticState.java
java/jpsgcs/alun/random/DensityFunction.java
java/jpsgcs/alun/random/MarkovChain.java
java/jpsgcs/alun/random/BetaRV.java
java/jpsgcs/alun/random/RandomEngine.java
java/jpsgcs/alun/random/CauchyRV.java
java/jpsgcs/alun/random/Rejection.java
java/jpsgcs/alun/random/ChengFeast.java
java/jpsgcs/alun/random/Envelope.java
java/jpsgcs/alun/random/GaussianRV.java
java/jpsgcs/alun/random/MetropolitanMC.java
java/jpsgcs/alun/random/RatioRegion.java
java/jpsgcs/alun/random/Metropolis.java
java/jpsgcs/alun/random/NormalRV.java
java/jpsgcs/alun/random/PoissonRV.java
java/jpsgcs/alun/random/NegativeBinomialRV.java
java/jpsgcs/alun/random/RandomColor.java
java/jpsgcs/alun/random/MarkovState.java
java/jpsgcs/alun/random/IntWithReplacement.java
java/jpsgcs/alun/random/ChiSquaredRV.java
java/jpsgcs/alun/random/PopulationCount.java
java/jpsgcs/alun/random/Point.java
java/jpsgcs/alun/random/DegenerateRV.java
java/jpsgcs/alun/random/ExponentialMixture.java
java/jpsgcs/alun/random/DiscreteStochasticProcess.java
java/jpsgcs/alun/random/AdaptiveRejection.java
java/jpsgcs/alun/random/GenerationMethod.java
java/jpsgcs/alun/random/CongruentialGenerator.java
java/jpsgcs/alun/random/LogConcave.java
java/jpsgcs/alun/random/RandomPermutation.java
java/jpsgcs/alun/random/RandomObject.java
java/jpsgcs/alun/random/Rand.java
java/jpsgcs/alun/random/BrownianMotion2D.java
java/jpsgcs/alun/random/PseudoRandomEngine.java
java/jpsgcs/alun/random/AliasRejection.java
java/jpsgcs/alun/random/ExponentialRV.java
java/jpsgcs/alun/random/Metropolitan.java
java/jpsgcs/alun/random/Locus2D.java
java/jpsgcs/alun/random/BinomialRV.java
java/jpsgcs/alun/random/Locus.java
java/jpsgcs/alun/random/IntegerMethod.java
java/jpsgcs/alun/random/ThrownString.java
java/jpsgcs/alun/random/RenewalCount.java
java/jpsgcs/alun/random/Count.java
java/jpsgcs/alun/random/FiniteStateMC.java
java/jpsgcs/alun/random/BuiltInGenerator.java
java/jpsgcs/alun/random/GeometricRV.java
java/jpsgcs/alun/random/VonMisesRV.java
java/jpsgcs/alun/random/Mixture.java
java/jpsgcs/alun/random/HotBitsEngine.java
java/jpsgcs/alun/random/DifferentiableLogConcave.java
java/jpsgcs/alun/random/ParameterException.java
java/jpsgcs/alun/random/StudentsRV.java
java/jpsgcs/alun/random/DegenerateIntegerRV.java
java/jpsgcs/alun/random/RatioOfUniforms.java
java/jpsgcs/alun/random/Inversion.java
java/jpsgcs/alun/random/RandomVariable.java
java/jpsgcs/alun/random/PoissonProcess.java
java/jpsgcs/alun/random/Line.java
java/jpsgcs/alun/random/IntegerValuedRV.java
java/jpsgcs/alun/random/ExponentialSwitching.java
java/jpsgcs/alun/random/RandomBag.java
java/jpsgcs/alun/random/GeneralExponentialRV.java
java/jpsgcs/alun/random/BernoulliRV.java
java/jpsgcs/alun/random/RandomWalk.java
java/jpsgcs/alun/random/InverseDistribution.java
java/jpsgcs/alun/random/RenewalProcess.java
java/jpsgcs/alun/random/Sampling.java
java/jpsgcs/alun/random/BirthAndDeathProcess.java
java/jpsgcs/alun/random/FisherRV.java
java/jpsgcs/alun/random/AhrensBinomial.java
java/jpsgcs/alun/random/UniformIntegerRV.java
java/jpsgcs/alun/random/UniformRV.java
java/jpsgcs/alun/graph
java/jpsgcs/alun/graph/LocatedGraph.java
java/jpsgcs/alun/graph/Network.java
java/jpsgcs/alun/graph/Derivatives.java
java/jpsgcs/alun/graph/LocalLocator.java
java/jpsgcs/alun/graph/MutableGraph.java
java/jpsgcs/alun/graph/GraphLocator.java
java/jpsgcs/alun/graph/Parameter.java
java/jpsgcs/alun/graph/LocatedMaskedGraph.java
java/jpsgcs/alun/graph/MaskedGraph.java
java/jpsgcs/alun/graph/Point.java
java/jpsgcs/alun/graph/Graph.java
java/jpsgcs/alun/graph/NetworkMask.java
java/jpsgcs/alun/graph/Graphs.java
java/jpsgcs/alun/graph/GraphSkeleton.java
java/jpsgcs/alun/graph/RootedLocalLocator.java
java/jpsgcs/alun/graph/IdentityNetwork.java
java/jpsgcs/alun/graph/DAGLocator.java
java/jpsgcs/alun/hashing
java/jpsgcs/alun/hashing/RandomIdentitySet.java
java/jpsgcs/alun/hashing/IdentityHashMap.java
java/jpsgcs/alun/markov
java/jpsgcs/alun/markov/MultiVariable.java
java/jpsgcs/alun/markov/Function.java
java/jpsgcs/alun/markov/MarkovRandomField.java
java/jpsgcs/alun/markov/DenseTable.java
java/jpsgcs/alun/markov/Functions.java
java/jpsgcs/alun/markov/ModelInfo.java
java/jpsgcs/alun/markov/Iterable.java
java/jpsgcs/alun/markov/Potential.java
java/jpsgcs/alun/markov/GraphicalModel.java
java/jpsgcs/alun/markov/Trivial.java
java/jpsgcs/alun/markov/Variable.java
java/jpsgcs/alun/markov/Table.java
java/jpsgcs/alun/genio
java/jpsgcs/alun/genio/PedigreeData.java
java/jpsgcs/alun/genio/Pedigree.java
java/jpsgcs/alun/genio/Family.java
java/jpsgcs/alun/genio/GeneticDataSource.java
java/jpsgcs/alun/genio/ParameterData.java
java/jpsgcs/alun/genio/BasicGeneticData.java
java/jpsgcs/alun/animate
java/jpsgcs/alun/animate/TransformListener.java
java/jpsgcs/alun/animate/Loop.java
java/jpsgcs/alun/animate/BufferedCanvas.java
java/jpsgcs/alun/animate/MouseKeyListener.java
java/jpsgcs/alun/animate/ScrollWidget.java
java/jpsgcs/alun/animate/Paintable.java
java/jpsgcs/alun/animate/FrameQuitter.java
java/jpsgcs/alun/animate/ActiveCanvas.java
java/jpsgcs/alun/util
java/jpsgcs/alun/util/SafeRunnable.java
java/jpsgcs/alun/util/CartesianPoint.java
java/jpsgcs/alun/util/Pair.java
java/jpsgcs/alun/util/Monitor.java
java/jpsgcs/alun/util/InputFormatter.java
java/jpsgcs/alun/util/LinearCalibrator.java
java/jpsgcs/alun/util/StringFormatter.java
java/jpsgcs/alun/util/IntValue.java
java/jpsgcs/alun/util/SafeThread.java
java/jpsgcs/alun/util/RadixPlaneSorter.java
java/jpsgcs/alun/util/Triplet.java
java/jpsgcs/alun/util/IntDoubleItem.java
java/jpsgcs/alun/util/Lattice.java
java/jpsgcs/alun/util/IntArray.java
java/jpsgcs/alun/util/AlphaSet.java
java/jpsgcs/alun/util/DoubleValue.java
java/jpsgcs/alun/util/IntDoubleMap.java
java/jpsgcs/alun/util/RandomBag.java
java/jpsgcs/alun/util/GoldenSection.java
java/jpsgcs/alun/util/Main.java
java/jpsgcs/alun/util/Curve.java
java/jpsgcs/alun/pedapps
java/jpsgcs/alun/pedapps/GeneCounter.java
java/jpsgcs/alun/pedapps/Pedigrees.java
java/jpsgcs/alun/pedapps/GeneticMap.java
java/jpsgcs/alun/pedapps/Kinship.java
java/jpsgcs/alun/pedapps/GeneDropper.java
java/jpsgcs/alun/pedapps/CompleteHaplotypes.java
java/jpsgcs/alun/pedapps/AlleleSharing.java
java/jpsgcs/alun/pedapps/CompletingPenetrance.java
java/jpsgcs/alun/pedapps/TLods.java
java/jpsgcs/alun/pedapps/LocInfo.java
java/jpsgcs/alun/pedapps/MultiPoints.java
java/jpsgcs/alun/pedapps/PhaseKnownHaplotypes.java
java/jpsgcs/alun/pedapps/MarriageNodeGraph.java
java/jpsgcs/alun/pedapps/ErrorCount.java
java/jpsgcs/alun/linkage
java/jpsgcs/alun/linkage/LinkConstants.java
java/jpsgcs/alun/linkage/QuantitativeLocus.java
java/jpsgcs/alun/linkage/AffectionStatusPhenotype.java
java/jpsgcs/alun/linkage/QuantitativePhenotype.java
java/jpsgcs/alun/linkage/LinkageFormatter.java
java/jpsgcs/alun/linkage/LinkagePhenotype.java
java/jpsgcs/alun/linkage/LinkageInterface.java
java/jpsgcs/alun/linkage/AffectionStatusLocus.java
java/jpsgcs/alun/linkage/LinkageParameterData.java
java/jpsgcs/alun/linkage/LinkageLocus.java
java/jpsgcs/alun/linkage/SteppedLinkageData.java
java/jpsgcs/alun/linkage/LinkageDataSet.java
java/jpsgcs/alun/linkage/LinkageIndividual.java
java/jpsgcs/alun/linkage/TransposedPedigreeData.java
java/jpsgcs/alun/linkage/LinkageException.java
java/jpsgcs/alun/linkage/Linkage.java
java/jpsgcs/alun/linkage/NumberedAlleleLocus.java
java/jpsgcs/alun/linkage/NumberedAllelePhenotype.java
java/jpsgcs/alun/linkage/LinkagePedigreeData.java
java/jpsgcs/alun/jtree
java/jpsgcs/alun/jtree/Separator.java
java/jpsgcs/alun/jtree/MultinomialMLEScorer.java
java/jpsgcs/alun/jtree/Clique.java
java/jpsgcs/alun/jtree/DiscreteData.java
java/jpsgcs/alun/jtree/UniformDecomposable.java
java/jpsgcs/alun/jtree/GraphNotDecomposableException.java
java/jpsgcs/alun/jtree/IntegerMatrix.java
java/jpsgcs/alun/jtree/ProperIntervalJTree.java
java/jpsgcs/alun/jtree/JTree.java
java/jpsgcs/alun/jtree/JTrees.java
java/jpsgcs/alun/jtree/AbstractJTreeSampler.java
java/jpsgcs/alun/jtree/OnePairSampler.java
java/jpsgcs/alun/jtree/UniformJTree.java
java/jpsgcs/alun/jtree/OrderedJTree.java
java/jpsgcs/alun/jtree/JTreeSampler.java
java/jpsgcs/alun/jtree/DataMatrix.java
java/jpsgcs/alun/jtree/CliqueScorer.java
java/jpsgcs/alun/jtree/CardinalitySorter.java
java/jpsgcs/alun/jtree/PruferSorter.java
java/jpsgcs/alun/viewgraph
java/jpsgcs/alun/viewgraph/GraphListener.java
java/jpsgcs/alun/viewgraph/GraphFrame.java
java/jpsgcs/alun/viewgraph/PaintableGraph.java
java/jpsgcs/alun/viewgraph/VertexRepresentation.java
java/jpsgcs/alun/viewgraph/ParameterScrollWidget.java
java/jpsgcs/alun/viewgraph/GraphPanel.java
java/jpsgcs/alun/viewgraph/Blob.java
java/jpsgcs/alun/viewgraph/StringNode.java
java/jpsgcs/alun/viewgraph/GraphAnimator.java
java/jpsgcs/alun/gchap
java/jpsgcs/alun/gchap/MarkerPhenotype.java
java/jpsgcs/alun/gchap/Marker.java
java/jpsgcs/alun/gchap/SNP.java
java/jpsgcs/alun/gchap/MultiLocusObservation.java
java/jpsgcs/alun/gchap/Phenotype.java
java/jpsgcs/alun/gchap/Sorter.java
java/jpsgcs/alun/gchap/HashOfHash.java
java/jpsgcs/alun/gchap/Observation.java
java/jpsgcs/alun/gchap/Locus.java
java/jpsgcs/alun/gchap/MultiLocusTrait.java
java/jpsgcs/alun/gchap/MarkerObservation.java
java/jpsgcs/alun/gchap/MultiLocusPhenotype.java
java/jpsgcs/alun/gchap/GeneticTrait.java
java/jpsgcs/alun/gchap/Genotype.java
java/jpsgcs/alun/gchap/HapFormatter.java
java/jpsgcs/alun/gchap/MultiLocus.java
java/Heterozygosities.java
java/ViewPed.java
java/MakePed.java
java/FitGMLD.java
java/SelectPedigrees.java
java/TestRandom.java
java/GeneCountAlleles.java
java/HetLods.java
java/HapMapToLinkage.java
java/FitGM.java
java/HGS.java
java/overview.html
java/TwoPointLods.java
java/MakeProbands.java
java/ViewGraph.java
java/LocusLogLikelihoods.java
java/CheckPedigree.java
java/cMorgansToTheta.java
java/LinkageToPhase.java
java/CheckTriplets.java
java/ApproxGCHap.java
java/CheckFormat.java
java/ViewDAG.java
java/GeneDrops.java
java/McMultiPoints.java
java/SelectKindreds.java
java/TrimPed.java
java/ObligateErrors.java
java/TransposeLinkage.java
java/SGS.java
java/CompileLDModel.java
java/MaxTwoPointLods.java
java/Triangulate.java
java/McCheck.java
java/CliquesToAdj.java
DESCRIPTION
man
man/exdat.Rd
man/write.parfile.Rd
man/GeneDrops.Rd
man/write.pedfile.Rd
man/FitGMLD.Rd
man/rJPSGCS-package.Rd
man/read.pedfile.Rd
rJPSGCS documentation built on May 20, 2017, 12:03 a.m.

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