rJPSGCS: R-interface to Gene Drop Simulation from JPSGCS

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

Author
Sigal Blay [aut], Jinko Graham [aut], Brad McNeney [aut, cre], Annick Nembot-Simo [aut], Alun Thomas [ctb], Hin-Tak Leung [ctb]
Date of publication
2014-12-08 09:54:39
Maintainer
Brad McNeney <mcneney@sfu.ca>
License
GPL-3
Version
0.2-7

View on CRAN

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.

Files in this package

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