imputationKey: Get out key for IBD genotype imputations

In rohan-shah/mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Get out key for IBD genotype imputations

Usage

imputationKey(object, ...)

## S4 method for signature 'imputed'
imputationKey(object, ...)

## S4 method for signature 'geneticData'
imputationKey(object, ...)

## S4 method for signature 'mpcrossMapped'
imputationKey(object, ...)

Arguments

object	The object from which to get the imputation key.
...	Extra parameters. Currently only "experiment" is supported, letting the user extract the imputation map for a specific experiment.

Details

When IBD genotype imputation is performed using a population with finite generations of selfing, some of the imputed genotypes will be heterozygotes. However, the imputation code only returns a single value per line per genetic position. This key translates that value to a pair of founder alleles.

The key is a matrix with three columns. The first two columns represent founder alleles, and the third column gives the encoding for that particular pair of founder alleles.

Value

Key giving the encoding of heterozygotes, in the imputed IBD genotype data.

Examples

pedigree <- eightParentPedigreeRandomFunnels(initialPopulationSize = 100, 
	selfingGenerations = 2, nSeeds = 1, intercrossingGenerations = 0)
selfing(pedigree) <- "finite"
#Generate map
map <- qtl::sim.map()
#Simulate data
cross <- simulateMPCross(map = map, pedigree = pedigree, mapFunction = haldane)
crossSNP <- cross + multiparentSNP(keepHets = TRUE)
crossMapped <- mpcrossMapped(crossSNP, map = map)
imputed <- imputeFounders(crossMapped, errorProb = 0.01)
#An imputed IBD genotype of 1 indicates a homozygote for founder 1
#An imputed IBD genotype of 9 indicates a heterozygote for founders 1 and 2
#etc
head(imputationKey(imputed))

rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.