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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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Version

Install

install.packages('mpMap2')

Monthly Downloads

7

Version

1.0.4

License

GPL-2

Maintainer

Rohan Shah

Last Published

September 11th, 2020

Functions in mpMap2 (1.0.4)

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