# Genetic Analysis of Multi-Parent Recombinant Inbred Lines

## Documentation for package ‘mpMap2’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J K L M N O P R S T W misc

## -- A --

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

## -- B --

backcrossPedigree | Generate a backcross pedigree which starts from inbred founders
biparentalDominant | Make markers in a biparental cross dominant

## -- C --

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

## -- D --

detailedPedigree | Pedigree for simulation
detailedPedigree-class | Pedigree for simulation

## -- E --

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

## -- F --

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.
finalNames-method | 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.
finals-method | 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
flatImputationMapNames-method | 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.
founderNames-method | 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.
founders-method | 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

## -- G --

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

## -- H --

haldane | Map functions
haldaneToRf | Map functions
hetData | Get the encoding of marker heterozygotes
hetData-method | Get the encoding of marker heterozygotes
hetsForSNPMarkers | Create heterozygote encodings for SNP markers

## -- I --

imputationData | Get out the IBD genotype imputation data
imputationData-method | Get out the IBD genotype imputation data
imputationKey | Get out key for IBD genotype imputations
imputationKey-method | Get out key for IBD genotype imputations
imputationMap | Get map used for IBD genotype imputation
imputationMap-method | 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-method | Initialize method which can skip the validity check

## -- J --

jitterMap | Add noise to marker positions

## -- K --

kosambi | Map functions
kosambiToRf | Map functions

## -- L --

lineNames | Get or set the genetic line names
lineNames-method | Get the genetic line names
lineNames-method | Get or set the genetic line names of a pedigree
lineNames<- | Get or set the genetic line names of a pedigree
lineNames<--method | 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

## -- M --

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.
markers-method | 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

## -- N --

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.
nFounders-method | 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.
nLines-method | 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.
nMarkers-method | 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

## -- O --

omp_get_num_threads | Get or set number of threads for OpenMP
omp_set_num_threads | Get or set number of threads for OpenMP
orderCross | Order markers Order markers within linkage groups using simulated annealing

## -- P --

pedigree | Create a pedigree object
pedigree-class | Pedigree class
pedigreeGraph-class | Graph for a pedigree
pedigreeToGraph | Convert pedigree to a graph
plot-method | Plot chi-squared statistics for independence
plot-method | Plot the graph of a pedigree
plot-method | Plot methods
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
probabilityData-method | Get IBD probability data

## -- R --

redact | Redact sensitive information This function redacts possibly sensitive information from objects, resulting in an object that is safe to publish.
redact-method | 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
rfToHaldane | Map functions
rfToKosambi | Map functions
rilPedigree | Generate a two-parent RIL pedigree which starts from inbred founders

## -- S --

selfing | Get or set a pedigree to have finite or infinite generations of selfing
selfing-method | Get or set a pedigree to have finite or infinite generations of selfing
selfing<- | Get or set a pedigree to have finite or infinite generations of selfing
selfing<--method | Get or set a pedigree to have finite or infinite generations of selfing
simulatedFourParentData | Simulated data from a four-parent population.
simulatedFourParentMap | Simulated data from a four-parent population.
simulateMPCross | Simulate data from multi-parent designs
sixteenParentPedigreeRandomFunnels | Generate a sixteen-parent pedigree
stripPedigree | Strip pedigree of unneccessary lines
subset-method | Subset data

## -- T --

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

## -- W --

wsnp_Ku_rep_c103074_89904851 | Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851

## -- misc --

+-method | Combine mpcross objects
+-method | Internal operators for mpMap2
.geneticData | Object containing the genetic data for a population
.mpcross | A collection of multi-parent populations without a genetic map
.mpcrossMapped | A collection of multi-parent populations with a genetic map
.mpcrossRF | A collection of multi-parent populations with recombination fraction estimates
.pedigreeGraph | Graph for a pedigree
.probabilities | Identity-by-descent genotype probabilities
[-method | Internal operators for mpMap2