A B C D E F G H I J K L M N O P R S T W misc
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 | Pedigree for simulation |
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. |
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 |
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 |
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 |
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 |
jitterMap | Add noise to marker positions |
kosambi | Map functions |
kosambiToRf | Map functions |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
+-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 |