+,mpcrossMapped,mpcrossMapped-method
                        Combine mpcross objects
[,rawSymmetricMatrix,index,index,logical-method
                        Internal operators for mpMap2
addExtraMarkerFromRawCall
                        Add an extra marker from raw calling data
addExtraMarkers         Add extra markers
as.mpInterval           Convert mpcross object to MPWGAIM format
assignFounderPattern    Set founder genotypes
backcrossPedigree       Generate a backcross pedigree which starts from
                        inbred founders
biparentalDominant      Make markers in a biparental cross dominant
callFromMap             Call markers based on an existing map
changeMarkerPosition    Change the position of a single marker
clusterOrderCross       Group markers into blocks and arrange those
                        blocks
combineKeepRF           Combine mpcross objects, keeping recombination
                        fraction data
computeAllEpistaticChiSquared
                        Compute chi-squared test statistics for
                        independence
computeGenotypeProbabilities
                        Compute IBD genotype probabilities
detailedPedigree-class
                        Pedigree for simulation
eightParentPedigreeImproperFunnels
                        Generate an eight-parent pedigree with improper
                        funnels
eightParentPedigreeRandomFunnels
                        Generate an eight-parent pedigree, using random
                        funnels
eightParentPedigreeSingleFunnel
                        Generate an eight-parent pedigree, using a
                        single funnel
eightParentSubsetMap    Genetic map and genetic data from an 8-parent
                        MAGIC population.
estimateMap             Estimate map distances
estimateMapFromImputation
                        Re-estimate large gaps in a genetic map from
                        IBD genotype imputations
estimateRF              Estimate pairwise recombination fractions This
                        function estimates the recombination fractions
                        between all pairs of markers in the input
                        object. The recombination fractions are
                        estimated using numerical maximum likelihood,
                        and a grid search. Because every estimate will
                        be one of the input test values, the estimates
                        can be stored efficiently with a single byte
                        per estimate.
estimateRFSingleDesign
                        Estimate pairwise recombination fractions
existingLocalisationStatistics
                        Localisation statistics for example of
                        callFromMap
expand                  Expand markers contained within object
exportMapToPretzl       Export genetic map to Pretzl
extraImputationPoints   Get out non-marker positions used for IBD
                        genotype imputation
f2Pedigree              Generate an F2 pedigree which starts from
                        inbred founders
finalNames              Names of genetic lines Return the names of the
                        genetic lines If the 'mpcross' object contains
                        a single experiment a vector of names of
                        genetic lines is returned. The names of the
                        founding lines for the population are excluded.
                        If an 'mpcross' object contains multiple
                        experiments a list of vectors of names is
                        returned.
finals                  Genetic data for final lines Return the genetic
                        data matrix for the final lines If the
                        'mpcross' object contains a single experiment a
                        matrix is returned, with rows corresponding to
                        genotyped lines and columns corresponding to
                        markers. The founding lines of the population
                        are excluded from this matrix. If an 'mpcross'
                        object contains multiple experiments a list of
                        such matrices is returned, one for each
                        experiment.
fixedNumberOfFounderAlleles
                        Convert fully informative experiment to one
                        with a fixed number of alleles per marker
flatImputationMapNames
                        Get names of positions for IBD genotype
                        imputation
formGroups              Form linkage groups
founderNames            Names of founding genetic lines Return the
                        names of the founding genetic lines If the
                        'mpcross' object contains a single experiment a
                        vector of names of genetic lines is returned.
                        If an 'mpcross' object contains multiple
                        experiments a list of vectors of names is
                        returned.
founders                Genetic data for founding lines Return the
                        genetic data matrix for the founding lines If
                        the 'mpcross' object contains a single
                        experiment a matrix is returned, with rows
                        corresponding to founding lines and columns
                        corresponding to markers. If an 'mpcross'
                        object contains multiple experiments a list of
                        such matrices is returned, one for each
                        experiment.
fourParentPedigreeRandomFunnels
                        Generate a four-parent pedigree
fourParentPedigreeSingleFunnel
                        Generate a four-parent pedigree
fromMpMap               Convert from mpMap format to mpMap2 format
generateGridPositions   Specify an equally spaced grid of genetic
                        positions
generateIntervalMidPoints
                        Specify interval midpoints
geneticData-class       Object containing the genetic data for a
                        population
getAllFunnels           Get funnels
getAllFunnelsIncAIC     Get all funnels, including AIC lines
getChromosomes          Get chromosome assignment per marker
getIntercrossingAndSelfingGenerations
                        Identify number of generations of intercrossing
                        and selfing, per genetic line
getPositions            Get positions of genetic markers
hetData                 Get the encoding of marker heterozygotes
hetsForSNPMarkers       Create heterozygote encodings for SNP markers
imputationData          Get out the IBD genotype imputation data
imputationKey           Get out key for IBD genotype imputations
imputationMap           Get map used for IBD genotype imputation
impute                  Impute missing recombination fraction estimates
imputeFounders          Impute underlying genotypes
infiniteSelfing         Create allele encoding corresponding to
                        infinite generations of selfing
initialize,canSkipValidity-method
                        Initialize method which can skip the validity
                        check
jitterMap               Add noise to marker positions
lineNames               Get or set the genetic line names
lineNames,mpcross-method
                        Get the genetic line names
lineNames<-             Get or set the genetic line names of a pedigree
linesByNames            Extract pedigree by names
listCodingErrors        Generate a list of encoding errors
listCodingErrorsInfiniteSelfing
                        Generate a list of encoding errors assuming
                        infinite selfing
mapFunctions            Map functions
markers                 Genotyped markers Return the names of the
                        genotyped markers. If an 'mpcross' object
                        contains multiple experiments, all experiments
                        are required to have the same markers. So a
                        single vector of marker names is returned, in
                        all cases.
mpcross                 Create object of class mpcross
mpcross-class           A collection of multi-parent populations
                        without a genetic map
mpcrossMapped           Create object of class mpcrossMapped
mpcrossMapped-class     A collection of multi-parent populations with a
                        genetic map
mpcrossRF-class         A collection of multi-parent populations with
                        recombination fraction estimates
multiparentSNP          Convert all markers to SNP markers
nFounders               Number of genotyped markers Return the number
                        of genotyped markers in an object. If an
                        'mpcross' object contains multiple experiments,
                        one number is returned per experiment.
nLines                  Number of genotyped lines Return the number of
                        genotyped lines in an object. This includes
                        only the number of final lines genotyped in the
                        population, and does not include the founding
                        lines. If an 'mpcross' object contains multiple
                        experiments, one number is returned per
                        experiment.
nMarkers                Number of genotyped markers Return the number
                        of genotyped markers in an object. If an
                        'mpcross' object contains multiple experiments,
                        all experiments are required to have the same
                        markers. So only one number is returned, in all
                        cases.
normalPhenotype         Simulate normally distributed phenotype
omp_set_num_threads     Get or set number of threads for OpenMP
orderCross              Order markers Order markers within linkage
                        groups using simulated annealing
pedigree                Create a pedigree object
pedigree-class          Pedigree class
pedigreeGraph-class     Graph for a pedigree
pedigreeToGraph         Convert pedigree to a graph
plot,addExtraMarkersStatistics,ANY-method
                        Plot chi-squared statistics for independence
plot,mpcross,ANY-method
                        Plot methods
plot,pedigreeGraph,ANY-method
                        Plot the graph of a pedigree
plotMosaic              Plot estimated genetic composition of lines
plotProbabilities       Plot genetic composition across the genome
probabilities-class     Identity-by-descent genotype probabilities
probabilityData         Get IBD probability data
redact                  Redact sensitive information This function
                        redacts possibly sensitive information from
                        objects, resulting in an object that is safe to
                        publish.
removeHets              Remove heterozygotes
reverseChromosomes      Reverse the order of the specified chromosomes
rilPedigree             Generate a two-parent RIL pedigree which starts
                        from inbred founders
selfing<-               Get or set a pedigree to have finite or
                        infinite generations of selfing
simulateMPCross         Simulate data from multi-parent designs
simulatedFourParentData
                        Simulated data from a four-parent population.
sixteenParentPedigreeRandomFunnels
                        Generate a sixteen-parent pedigree
stripPedigree           Strip pedigree of unneccessary lines
subset,imputed-method   Subset data
testDistortion          Test for distortion using IBD genotype
                        probabilities
toMpMap                 Convert to mpMap format
transposeProbabilities
                        Transpose IBD probabilities
twoParentPedigree       Generate a two-parent pedigree which starts
                        from inbred founders
wsnp_Ku_rep_c103074_89904851
                        Raw genotyping data for marker
                        wsnp_Ku_rep_c103074_89904851
