Man pages for mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines

addExtraMarkerFromRawCallAdd an extra marker from raw calling data
addExtraMarkersAdd extra markers
as.mpIntervalConvert mpcross object to MPWGAIM format
assignFounderPatternSet founder genotypes
backcrossPedigreeGenerate a backcross pedigree which starts from inbred...
biparentalDominantMake markers in a biparental cross dominant
callFromMapCall markers based on an existing map
changeMarkerPositionChange the position of a single marker
clusterOrderCrossGroup markers into blocks and arrange those blocks
combineKeepRFCombine mpcross objects, keeping recombination fraction data
combineMpcrossCombine mpcross objects
computeAllEpistaticChiSquaredCompute chi-squared test statistics for independence
computeGenotypeProbabilitiesCompute IBD genotype probabilities
detailedPedigree-classPedigree for simulation
eightParentPedigreeImproperFunnelsGenerate an eight-parent pedigree with improper funnels
eightParentPedigreeRandomFunnelsGenerate an eight-parent pedigree, using random funnels
eightParentPedigreeSingleFunnelGenerate an eight-parent pedigree, using a single funnel
eightParentSubsetMapGenetic map and genetic data from an 8-parent MAGIC...
estimateMapEstimate map distances
estimateMapFromImputationRe-estimate large gaps in a genetic map from IBD genotype...
estimateRFEstimate pairwise recombination fractions This function...
estimateRFSingleDesignEstimate pairwise recombination fractions
existingLocalisationStatisticsLocalisation statistics for example of callFromMap
expandExpand markers contained within object
exportMapToPretzlExport genetic map to Pretzl
extraImputationPointsGet out non-marker positions used for IBD genotype imputation
f2PedigreeGenerate an F2 pedigree which starts from inbred founders
finalNamesNames of genetic lines Return the names of the genetic lines...
finalsGenetic data for final lines Return the genetic data matrix...
fixedNumberOfFounderAllelesConvert fully informative experiment to one with a fixed...
flatImputationMapNamesGet names of positions for IBD genotype imputation
formGroupsForm linkage groups
founderNamesNames of founding genetic lines Return the names of the...
foundersGenetic data for founding lines Return the genetic data...
fourParentPedigreeRandomFunnelsGenerate a four-parent pedigree
fourParentPedigreeSingleFunnelGenerate a four-parent pedigree
fromMpMapConvert from mpMap format to mpMap2 format
generateGridPositionsSpecify an equally spaced grid of genetic positions
generateIntervalMidPointsSpecify interval midpoints
geneticData-classObject containing the genetic data for a population
getAllFunnelsGet funnels
getAllFunnelsIncAICGet all funnels, including AIC lines
getChromosomesGet chromosome assignment per marker
getIntercrossingAndSelfingGenerationsIdentify number of generations of intercrossing and selfing,...
getPositionsGet positions of genetic markers
hetDataGet the encoding of marker heterozygotes
hetsForSNPMarkersCreate heterozygote encodings for SNP markers
imputationDataGet out the IBD genotype imputation data
imputationKeyGet out key for IBD genotype imputations
imputationMapGet map used for IBD genotype imputation
imputeImpute missing recombination fraction estimates
imputeFoundersImpute underlying genotypes
infiniteSelfingCreate allele encoding corresponding to infinite generations...
initializeInitialize method which can skip the validity check
internalOperatorsInternal operators for mpMap2
jitterMapAdd noise to marker positions
lineNamesGenericGet or set the genetic line names
lineNamesMpcrossGet the genetic line names
lineNamesPedigreeGet or set the genetic line names of a pedigree
linesByNamesExtract pedigree by names
listCodingErrorsGenerate a list of encoding errors
listCodingErrorsInfiniteSelfingGenerate a list of encoding errors assuming infinite selfing
mapFunctionsMap functions
markersGenotyped markers Return the names of the genotyped markers....
mpcrossCreate object of class mpcross
mpcross-classA collection of multi-parent populations without a genetic...
mpcrossMappedCreate object of class mpcrossMapped
mpcrossMapped-classA collection of multi-parent populations with a genetic map
mpcrossRF-classA collection of multi-parent populations with recombination...
multiparentSNPConvert all markers to SNP markers
nFoundersNumber of genotyped markers Return the number of genotyped...
nLinesNumber of genotyped lines Return the number of genotyped...
nMarkersNumber of genotyped markers Return the number of genotyped...
normalPhenotypeSimulate normally distributed phenotype
openmpGet or set number of threads for OpenMP
orderCrossOrder markers Order markers within linkage groups using...
pedigreeCreate a pedigree object
pedigree-classPedigree class
pedigreeGraph-classGraph for a pedigree
pedigreeToGraphConvert pedigree to a graph
plotPlot methods
plot-addExtraMarkersStatistics-ANY-methodPlot chi-squared statistics for independence
plotMosaicPlot estimated genetic composition of lines
plot-pedigreeGraph-ANY-methodPlot the graph of a pedigree
plotProbabilitiesPlot genetic composition across the genome
probabilities-classIdentity-by-descent genotype probabilities
probabilityDataGet IBD probability data
redactRedact sensitive information This function redacts possibly...
removeHetsRemove heterozygotes
reverseChromosomesReverse the order of the specified chromosomes
rilPedigreeGenerate a two-parent RIL pedigree which starts from inbred...
selfingGet or set a pedigree to have finite or infinite generations...
simulatedFourParentDataSimulated data from a four-parent population.
simulateMPCrossSimulate data from multi-parent designs
sixteenParentPedigreeRandomFunnelsGenerate a sixteen-parent pedigree
stripPedigreeStrip pedigree of unneccessary lines
subsetSubset data
testDistortionTest for distortion using IBD genotype probabilities
toMpMapConvert to mpMap format
transposeProbabilitiesTranspose IBD probabilities
twoParentPedigreeGenerate a two-parent pedigree which starts from inbred...
wsnp_Ku_rep_c103074_89904851Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851
mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.