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 |
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