Package: mpMap2
Type: Package
Title: Genetic Analysis of Multi-Parent Recombinant Inbred Lines
Version: 1.0.2
Date: 2020-04-06
Author: Rohan Shah [aut, cre],
  Emma Huang [aut],
  Matthew Morell [ctb],
  Alex Whan [ctb],
  Colin Cavanagh [ctb]
Authors@R: c(person("Rohan", "Shah", role = c("aut", "cre"), email = "cran@bookshah.com"),
              person("Emma", "Huang", role = c("aut")),
	      person("Matthew", "Morell", role = "ctb"),
	      person("Alex", "Whan", role = "ctb"),
	      person("Colin", "Cavanagh", role = "ctb"))
Maintainer: Rohan Shah <cran@bookshah.com>
Description: Constructing linkage maps, reconstructing haplotypes,
    estimating linkage disequilibrium and quantitative trait loci
    (QTL) mapping in multi-parent Recombinant Inbred Lines designs.
License: GPL-2
SystemRequirements: C++11
LazyLoad: yes
Depends: R (>= 3.5.0)
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown, gridExtra, Heatplus
Imports: ggplot2, Matrix, methods, qtl, igraph, fastcluster, pryr,
        nnls, RColorBrewer, jsonlite, progress, stats, sn, car
RoxygenNote: 7.0.2
Collate: 'Pillai.R' 'Rcpp_exceptions.R' 'map-class.R'
        'addExtraMarkerFromRawCall.R' 'addExtraMarkers.R'
        'canSkipValidity.R' 'pedigree-class.R' 'hetData-class.R'
        'geneticData-class.R' 'lg-class.R' 'rawSymmetricMatrix.R'
        'rf-class.R' 'mpcross-class.R' 'additionOperators.R'
        'as.mpInterval.R' 'assignFounderPattern.R'
        'assignFounderPatternPrototype.R' 'backcrossPedigree.R'
        'biparentalDominant.R' 'callFromMap.R' 'changeMarkerPosition.R'
        'combineGenotypes.R' 'combineKeepRF.R'
        'compressedProbabilities.R' 'computeAllEpistaticChiSquared.R'
        'computeGenotypeProbabilities.R' 'createSNPTemplate.R'
        'detailedPedigree-class.R' 'eightWayPedigreeImproperFunnels.R'
        'eightWayPedigreeRandomFunnels.R'
        'eightWayPedigreeSingleFunnel.R' 'estimateMap.R'
        'estimateMapFromImputation.R' 'estimateRF.R'
        'estimateRFSingleDesign.R' 'expand.R' 'expandedProbabilities.R'
        'exportMapToPretzl.R' 'extraImputationPoints.R' 'f2Pedigree.R'
        'finals.R' 'fixedNumberOfFounderAlleles.R' 'formGroups.R'
        'founders.R' 'fourParentPedigreeRandomFunnels.R'
        'fourParentPedigreeSingleFunnel.R' 'fullHetData.R'
        'generateGridPositions.R' 'generateIntervalMidPoints.R'
        'getAllFunnels.R' 'getChromosomes.R'
        'getIntercrossingAndSelfingGenerations.R' 'getPositions.R'
        'hetData.R' 'identC.R' 'imputationGenerics.R' 'impute.R'
        'imputeFounders.R' 'jitterMap.R' 'lineNames.R'
        'listCodingErrors.R' 'mapFunctions.R' 'markers.R' 'mpcross.R'
        'multiparentSNP.R' 'multiparentSNPPrototype.R' 'nFounders.R'
        'nLines.R' 'nMarkers.R' 'num_threads.R' 'orderCross.R'
        'pedigree.R' 'pedigreeGraph-class.R' 'pedigreeGraph.R'
        'pedigreeToGraph.R' 'plot.R' 'plotMosaic.R'
        'plotProbabilities.R' 'print.R' 'probabilityData.R'
        'purdyToPedigree.R' 'redact.R' 'removeHets.R'
        'reorderPedigree.R' 'reverseChromosomes.R' 'rilPedigree.R'
        'roxygen.R' 'selfing.R' 'show.R' 'simulateMPCross.R'
        'simulatePhenotypes.R' 'singleLocusProbabilities.R'
        'sixteenParentPedigreeRandomFunnels.R' 'stripPedigree.R'
        'subset.R' 'testDistortion.R' 'toMpMap.R'
        'transposeProbabilities.R' 'twoParentPedigree.R' 'validation.R'
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-04-06 10:56:26 UTC; rshah
Repository: CRAN
Date/Publication: 2020-04-07 15:00:14 UTC
Built: R 4.0.0; x86_64-w64-mingw32; 2020-04-10 12:36:39 UTC; windows
Archs: i386, x64
