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DESCRIPTION
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DESCRIPTION
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Package: mpMap2
Type: Package
Title: Genetic Analysis of Multi-Parent Recombinant Inbred Lines
Version: 1.0.3
Date: 2020-04-23
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 = "[email protected]"),
person("Emma", "Huang", role = c("aut")),
person("Matthew", "Morell", role = "ctb"),
person("Alex", "Whan", role = "ctb"),
person("Colin", "Cavanagh", role = "ctb"))
Maintainer: Rohan Shah <[email protected]>
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