Man pages for rohan-shah/mpMap2
Genetic Analysis of Multi-Parent Recombinant Inbred Lines
| 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... |
| 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 |
| combineMpcross | Combine mpcross objects |
| 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... |
| estimateMap | Estimate map distances |
| estimateMapFromImputation | Re-estimate large gaps in a genetic map from IBD genotype... |
| estimateRF | Estimate pairwise recombination fractions This function... |
| 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... |
| finals | Genetic data for final lines Return the genetic data matrix... |
| fixedNumberOfFounderAlleles | Convert fully informative experiment to one with a fixed... |
| flatImputationMapNames | Get names of positions for IBD genotype imputation |
| formGroups | Form linkage groups |
| founderNames | Names of founding genetic lines Return the names of the... |
| founders | Genetic data for founding lines Return the genetic data... |
| 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,... |
| 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... |
| initialize | Initialize method which can skip the validity check |
| internalOperators | Internal operators for mpMap2 |
| jitterMap | Add noise to marker positions |
| lineNamesGeneric | Get or set the genetic line names |
| lineNamesMpcross | Get the genetic line names |
| lineNamesPedigree | 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.... |
| mpcross | Create object of class mpcross |
| mpcross-class | A collection of multi-parent populations without a genetic... |
| 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... |
| multiparentSNP | Convert all markers to SNP markers |
| nFounders | Number of genotyped markers Return the number of genotyped... |
| nLines | Number of genotyped lines Return the number of genotyped... |
| nMarkers | Number of genotyped markers Return the number of genotyped... |
| normalPhenotype | Simulate normally distributed phenotype |
| openmp | Get or set number of threads for OpenMP |
| orderCross | Order markers Order markers within linkage groups using... |
| pedigree | Create a pedigree object |
| pedigree-class | Pedigree class |
| pedigreeGraph-class | Graph for a pedigree |
| pedigreeToGraph | Convert pedigree to a graph |
| plot | Plot methods |
| plot-addExtraMarkersStatistics-ANY-method | Plot chi-squared statistics for independence |
| plotMosaic | Plot estimated genetic composition of lines |
| plot-pedigreeGraph-ANY-method | Plot the graph of a pedigree |
| 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... |
| removeHets | Remove heterozygotes |
| reverseChromosomes | Reverse the order of the specified chromosomes |
| rilPedigree | Generate a two-parent RIL pedigree which starts from inbred... |
| selfing | Get or set a pedigree to have finite or infinite generations... |
| simulatedFourParentData | 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 | 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... |
| wsnp_Ku_rep_c103074_89904851 | Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851 |
