Files in mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines

MD5

NAMESPACE

DESCRIPTION

build/vignette.rds

src/viterbiFiniteSelfingApplyIntercrossing.h

src/joinMapWithExtra.cpp

src/intercrossingAndSelfingGenerations.cpp

src/probabilities16.h

src/compressedProbabilities_RInterface.cpp

src/probabilities16.cpp

src/generateKeys.h

src/computeAllEpistaticChiSquared.cpp

src/crc32.h

src/combineGenotypes.h

src/stripPedigree.h

src/recodeFoundersFinalsHets.cpp

src/getFunnel.h

src/arsaRawREntryPoint.cpp

src/multiparentSNP.h

src/orderFunnel.cpp

src/markerPatternsToUniqueValues.h

src/identC.cpp

src/generateDesignMatrix.cpp

src/reorderPedigree.h

src/funnelsToUniqueValues.h

src/estimateRFSingleDesignInternal.h

src/generateGenotypes.h

src/probabilities.h

src/estimateRFSingleDesign.cpp

src/expandedProbabilities_RInterface.cpp

src/removeHets.h

src/combineGenotypes.cpp

src/funnelHaplotypeToMarkerInfiniteSelfing.h

src/arsa.h

src/intercrossingHaplotypeToMarkerFiniteSelfing.h

src/singleLocusProbabilities_RInterface.cpp

src/dspMatrix.h

src/fourParentPedigreeRandomFunnels.cpp

src/viterbiFiniteSelfingApplyFunnel.h

src/forwardsBackwardsFiniteSelfingApplyIntercrossing.h

src/fourParentPedigreeSingleFunnel.h

src/probabilities4.cpp

src/order.cpp

src/assignFounderPattern.cpp

src/imputeFounders.cpp

src/getMinAIGenerations.h

src/computeAllEpistaticChiSquared.h

src/mpMap2_openmp.h

src/rawSymmetricMatrix.cpp

src/viterbiInfiniteSelfingApplyFunnel.h

src/parsePurdy.h

src/replaceHetsWithNA.cpp

src/matrices.h

src/testDistortion.h

src/removeHets.cpp

src/sixteenParentPedigreeRandomFunnels.cpp

src/probabilities2.h

src/estimateRF.h

src/generateDesignMatrix.h

src/estimateRFCheckFunnels.h

src/crc32.cpp

src/arsaRaw.cpp

src/funnelsToUniqueValues.cpp

src/forwardsBackwards.h

src/getAllFunnelsIncAIC.cpp

src/singleLocusProbabilities_RInterface.h

src/probabilities8.cpp

src/preClusterStep.cpp

src/fourParentPedigreeSingleFunnel.cpp

src/transposeProbabilities.h

src/mapFunctions.h

src/warnings.cpp

src/alleleDataErrors.h

src/parsePurdy.cpp

src/estimateRFSingleDesign.h

src/estimateRFCheckFunnels.cpp

src/intercrossingAndSelfingGenerations.h

src/sortPedigreeLineNames.h

src/generateGenotypes.cpp

src/array2.h

src/reorderPedigree.cpp

src/arsaRawREntryPoint.h

src/checkImputedBounds.cpp

src/checkHets.h

src/testDistortion.cpp

src/impossibleDataException.h

src/estimateRFSpecificDesign.h

src/checkHets.cpp

src/recodeFoundersFinalsHets.h

src/matrix.h

src/unitTypes.h

src/sortPedigreeLineNames.cpp

src/eightParentPedigreeImproperFunnels.h

src/joinMapWithExtra.h

src/probabilities4.h

src/alleleDataErrors.cpp

src/compressedProbabilities.h

src/mpMap2_openmp.cpp

src/getMinAIGenerations.cpp

src/rawSymmetricMatrix.h

src/probabilities8.h

src/checkImputedBounds.h

src/forwardsBackwardsInfiniteSelfingApplyIntercrossing.h

src/orderFunnel.h

src/combineRFDisjoint.h

src/assignFounderPattern.h

src/warnings.h

src/Makevars

src/getAllFunnels.h

src/viterbiFiniteSelfing.h

src/intercrossingHaplotypeToMarker.h

src/matrixChunks.h

src/generateKeys.cpp

src/identC.h

src/estimateRFSingleDesignInternal.cpp

src/preClusterStep.h

src/order.h

src/forwardsBackwardsFiniteSelfingApplyFunnel.h

src/estimateRF.cpp

src/sixteenParentPedigreeRandomFunnels.h

src/compressedProbabilities_RInterface.h

src/impute.cpp

src/transposeProbabilities.cpp

src/estimateRFSpecificDesign.cpp

src/imputeFounders.h

src/getAllFunnelsIncAIC.h

src/compressedProbabilities.cpp

src/arsaRaw.h

src/markerPatternsToUniqueValues.cpp

src/combineRFDisjoint.cpp

src/funnelHaplotypeToMarker.h

src/recodeHetsAsNA.h

src/intercrossingHaplotypeToMarkerInfiniteSelfing.h

src/computeGenotypeProbabilities.cpp

src/forwardsBackwardsInfiniteSelfingApplyFunnel.h

src/haldaneToRf.h

src/probabilitiesOther.h

src/convertGeneticData.cpp

src/forwardsBackwardsInfiniteSelfing.h

src/mapFunctions.cpp

src/viterbiInfiniteSelfing.h

src/constructLookupTable.h

src/computeGenotypeProbabilities.h

src/hclustMatrices.h

src/getFunnel.cpp

src/viterbiInfiniteSelfingApplyIntercrossing.h

src/throwInternal.cpp

src/convertGeneticData.h

src/multiparentSNP.cpp

src/stripPedigree.cpp

src/eightParentPedigreeSingleFunnel.h

src/dspMatrix.cpp

src/probabilities2.cpp

src/viterbi.h

src/funnelHaplotypeToMarkerFiniteSelfing.h

src/probabilities16IntermediateProbabilitiesMask.h

src/hclustMatrices.cpp

src/eightParentPedigreeImproperFunnels.cpp

src/eightParentPedigreeRandomFunnels.h

src/matrixChunks.cpp

src/fourParentPedigreeRandomFunnels.h

src/transformForMPWGAIM.cpp

src/arsa.cpp

src/eightParentPedigreeRandomFunnels.cpp

src/haldaneToRf.cpp

src/expandedProbabilities_RInterface.h

src/register.cpp

src/throwInternal.h

src/forwardsBackwardsFiniteSelfing.h

src/transformForMPWGAIM.h

src/impute.h

src/getAllFunnels.cpp

src/eightParentPedigreeSingleFunnel.cpp

data/callFromMapExampleLocalisationStatistics.RData

data/wsnp_Ku_rep_c103074_89904851.RData

data/simulatedFourParentData.RData

data/eightParentSubsetMap.RData

R/reverseChromosomes.R R/changeMarkerPosition.R R/expand.R R/fullHetData.R R/expandedProbabilities.R R/plotProbabilities.R R/selfing.R R/canSkipValidity.R R/callFromMap.R R/jitterMap.R R/pedigree.R R/eightWayPedigreeSingleFunnel.R R/mapFunctions.R R/getChromosomes.R R/map-class.R R/founders.R R/biparentalDominant.R R/rawSymmetricMatrix.R R/eightWayPedigreeRandomFunnels.R R/multiparentSNPPrototype.R R/markers.R R/testDistortion.R R/compressedProbabilities.R R/lg-class.R R/pedigreeToGraph.R R/rilPedigree.R R/computeAllEpistaticChiSquared.R R/pedigree-class.R R/simulateMPCross.R R/extraImputationPoints.R R/formGroups.R R/Pillai.R R/assignFounderPatternPrototype.R R/toMpMap.R R/roxygen.R R/transposeProbabilities.R R/additionOperators.R R/assignFounderPattern.R R/mpcross.R R/imputeFounders.R R/as.mpInterval.R R/num_threads.R R/addExtraMarkers.R R/nMarkers.R R/exportMapToPretzl.R R/plot.R R/getAllFunnels.R R/orderCross.R R/impute.R R/rf-class.R R/reorderPedigree.R R/generateGridPositions.R R/singleLocusProbabilities.R R/sixteenParentPedigreeRandomFunnels.R R/fourParentPedigreeSingleFunnel.R R/removeHets.R R/fixedNumberOfFounderAlleles.R R/nFounders.R R/estimateRF.R R/computeGenotypeProbabilities.R R/hetData.R R/fourParentPedigreeRandomFunnels.R R/listCodingErrors.R R/purdyToPedigree.R R/finals.R R/getIntercrossingAndSelfingGenerations.R R/validation.R R/subset.R R/multiparentSNP.R R/eightWayPedigreeImproperFunnels.R R/f2Pedigree.R R/lineNames.R R/createSNPTemplate.R R/combineKeepRF.R R/estimateRFSingleDesign.R R/probabilityData.R R/Rcpp_exceptions.R R/twoParentPedigree.R R/backcrossPedigree.R R/mpcross-class.R R/estimateMapFromImputation.R R/generateIntervalMidPoints.R R/pedigreeGraph-class.R R/show.R R/geneticData-class.R R/getPositions.R R/redact.R R/combineGenotypes.R R/detailedPedigree-class.R R/simulatePhenotypes.R R/pedigreeGraph.R R/print.R R/plotMosaic.R R/estimateMap.R R/stripPedigree.R R/imputationGenerics.R R/identC.R R/hetData-class.R R/nLines.R R/addExtraMarkerFromRawCall.R vignettes/funnelsIllustration.pdf vignettes/approximatelyFlatSingleFunnel00.pdf

vignettes/mpMap2.Rnw

vignettes/informativeSingleFunnel10.pdf vignettes/MAGIC8.pdf vignettes/informativeSingleFunnel00.pdf vignettes/approximatelyFlatSingleFunnel11.pdf vignettes/uninformativeSingleFunnel01.pdf vignettes/informativeSingleFunnel01.pdf vignettes/MAGIC4.pdf vignettes/approximatelyFlatSingleFunnel01.pdf vignettes/approximatelyFlatSingleFunnel10.pdf

vignettes/mpMap2.bib

inst/doc/mpMap2.Rnw

inst/doc/mpMap2.R inst/doc/mpMap2.pdf

inst/mathematica/finiteSelfingIntercrossing16Way.states

inst/mathematica/finiteSelfingIntercrossing8Way.nb

inst/mathematica/finiteSelfingIntercrossing4WaySingleFunnel.nb

inst/mathematica/finiteSelfingIntercrossing8WaySingleFunnel.nb

inst/mathematica/finiteSelfingIntercrossing8WaySinglePoint.nb

inst/mathematica/finiteSelfingIntercrossing4Way.nb

inst/mathematica/finiteSelfingIntercrossingF2.nb

inst/mathematica/finiteSelfingIntercrossing16Way.nb

inst/generateDatasets/generateExample1.R

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Files in mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines

R Package Documentation

Browse R Packages

We want your feedback!

mpMap2 Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Files in mpMap2 Genetic Analysis of Multi-Parent Recombinant Inbred Lines

R Package Documentation

Browse R Packages

We want your feedback!

mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Files in mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines