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mpMap2 (version 1.0.4)
Genetic Analysis of Multi-Parent Recombinant Inbred Lines
Description
Constructing linkage maps, reconstructing haplotypes, estimating linkage disequilibrium and quantitative trait loci (QTL) mapping in multi-parent Recombinant Inbred Lines designs.
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1.0.4
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Install
install.packages('mpMap2')
Monthly Downloads
50
Version
1.0.4
License
GPL-2
Maintainer
Rohan Shah
Last Published
September 11th, 2020
Functions in mpMap2 (1.0.4)
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backcrossPedigree
Generate a backcross pedigree which starts from inbred founders
biparentalDominant
Make markers in a biparental cross dominant
combineKeepRF
Combine mpcross objects, keeping recombination fraction data
assignFounderPattern
Set founder genotypes
addExtraMarkerFromRawCall
Add an extra marker from raw calling data
clusterOrderCross
Group markers into blocks and arrange those blocks
callFromMap
Call markers based on an existing map
as.mpInterval
Convert mpcross object to MPWGAIM format
addExtraMarkers
Add extra markers
changeMarkerPosition
Change the position of a single marker
+,mpcrossMapped,mpcrossMapped-method
Combine mpcross objects
eightParentPedigreeRandomFunnels
Generate an eight-parent pedigree, using random funnels
eightParentPedigreeImproperFunnels
Generate an eight-parent pedigree with improper funnels
eightParentPedigreeSingleFunnel
Generate an eight-parent pedigree, using a single funnel
eightParentSubsetMap
Genetic map and genetic data from an 8-parent MAGIC population.
fourParentPedigreeSingleFunnel
Generate a four-parent pedigree
fourParentPedigreeRandomFunnels
Generate a four-parent pedigree
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.
getChromosomes
Get chromosome assignment per marker
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.
existingLocalisationStatistics
Localisation statistics for example of callFromMap
expand
Expand markers contained within object
computeGenotypeProbabilities
Compute IBD genotype probabilities
estimateMap
Estimate map distances
fromMpMap
Convert from mpMap format to mpMap2 format
extraImputationPoints
Get out non-marker positions used for IBD genotype imputation
exportMapToPretzl
Export genetic map to Pretzl
generateGridPositions
Specify an equally spaced grid of genetic positions
getIntercrossingAndSelfingGenerations
Identify number of generations of intercrossing and selfing, per genetic line
imputationData
Get out the IBD genotype imputation data
infiniteSelfing
Create allele encoding corresponding to infinite generations of selfing
getPositions
Get positions of genetic markers
hetsForSNPMarkers
Create heterozygote encodings for SNP markers
hetData
Get the encoding of marker heterozygotes
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.
f2Pedigree
Generate an F2 pedigree which starts from inbred founders
flatImputationMapNames
Get names of positions for IBD genotype imputation
estimateMapFromImputation
Re-estimate large gaps in a genetic map from IBD genotype imputations
detailedPedigree-class
Pedigree for simulation
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.
imputeFounders
Impute underlying genotypes
multiparentSNP
Convert all markers to SNP markers
mpcrossRF-class
A collection of multi-parent populations with recombination fraction estimates
impute
Impute missing recombination fraction estimates
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.
computeAllEpistaticChiSquared
Compute chi-squared test statistics for independence
estimateRFSingleDesign
Estimate pairwise recombination fractions
imputationKey
Get out key for IBD genotype imputations
imputationMap
Get map used for IBD genotype imputation
fixedNumberOfFounderAlleles
Convert fully informative experiment to one with a fixed number of alleles per marker
initialize,canSkipValidity-method
Initialize method which can skip the validity check
[,rawSymmetricMatrix,index,index,logical-method
Internal operators for mpMap2
mpcross-class
A collection of multi-parent populations without a genetic map
jitterMap
Add noise to marker positions
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.
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.
mapFunctions
Map functions
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.
removeHets
Remove heterozygotes
reverseChromosomes
Reverse the order of the specified chromosomes
generateIntervalMidPoints
Specify interval midpoints
omp_set_num_threads
Get or set number of threads for OpenMP
formGroups
Form linkage groups
mpcross
Create object of class mpcross
pedigreeGraph-class
Graph for a pedigree
selfing<-
Get or set a pedigree to have finite or infinite generations of selfing
rilPedigree
Generate a two-parent RIL pedigree which starts from inbred founders
geneticData-class
Object containing the genetic data for a population
mpcrossMapped
Create object of class mpcrossMapped
linesByNames
Extract pedigree by names
lineNames<-
Get or set the genetic line names of a pedigree
mpcrossMapped-class
A collection of multi-parent populations with a genetic map
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.
lineNames
Get or set the genetic line names
listCodingErrors
Generate a list of encoding errors
listCodingErrorsInfiniteSelfing
Generate a list of encoding errors assuming infinite selfing
lineNames,mpcross-method
Get the genetic line names
redact
Redact sensitive information This function redacts possibly sensitive information from objects, resulting in an object that is safe to publish.
stripPedigree
Strip pedigree of unneccessary lines
probabilityData
Get IBD probability data
sixteenParentPedigreeRandomFunnels
Generate a sixteen-parent pedigree
orderCross
Order markers Order markers within linkage groups using simulated annealing
getAllFunnels
Get funnels
getAllFunnelsIncAIC
Get all funnels, including AIC lines
pedigree-class
Pedigree class
plot,mpcross,ANY-method
Plot methods
plotMosaic
Plot estimated genetic composition of lines
pedigree
Create a pedigree object
pedigreeToGraph
Convert pedigree to a graph
wsnp_Ku_rep_c103074_89904851
Raw genotyping data for marker wsnp_Ku_rep_c103074_89904851
simulatedFourParentData
Simulated data from a four-parent population.
twoParentPedigree
Generate a two-parent pedigree which starts from inbred founders
simulateMPCross
Simulate data from multi-parent designs
testDistortion
Test for distortion using IBD genotype probabilities
probabilities-class
Identity-by-descent genotype probabilities
plotProbabilities
Plot genetic composition across the genome
subset,imputed-method
Subset data
plot,addExtraMarkersStatistics,ANY-method
Plot chi-squared statistics for independence
normalPhenotype
Simulate normally distributed phenotype
plot,pedigreeGraph,ANY-method
Plot the graph of a pedigree
transposeProbabilities
Transpose IBD probabilities
toMpMap
Convert to mpMap format