Description Usage Arguments Details Value Examples
Get out key for IBD genotype imputations
1 2 3 4 5 6 7 8 9 10 | imputationKey(object, ...)
## S4 method for signature 'imputed'
imputationKey(object, ...)
## S4 method for signature 'geneticData'
imputationKey(object, ...)
## S4 method for signature 'mpcrossMapped'
imputationKey(object, ...)
|
object |
The object from which to get the imputation key. |
... |
Extra parameters. Currently only |
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.
Key giving the encoding of heterozygotes, in the imputed IBD genotype data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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))
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