context("genotype probability computation, four parents, infinite selfing")
test_that("Test zero generations of intercrossing",
{
testFunc <- function(map, pedigree)
{
#First check that with fully informative markers we get back the original data.
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane) + removeHets()
mapped <- new("mpcrossMapped", cross, map = map)
suppressWarnings(result <- computeGenotypeProbabilities(mapped))
genotypesFromProbabilities <- lapply(1:nLines(result), function(x)
{
apply(result@geneticData[[1]]@probabilities@data[(4*x-3):(4*x),], 2, which.max)
})
genotypesFromProbabilities <- do.call(rbind, genotypesFromProbabilities)
#The most probable founders should agree with the actual data, except for the case where the line really is hetrozygous.
expect_true(all((genotypesFromProbabilities == result@geneticData[[1]]@finals) | is.na(result@geneticData[[1]]@finals)))
}
map <- qtl::sim.map(len = c(100, 100), n.mar = 101, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
pedigrees <- list()
pedigrees[[1]] <- fourParentPedigreeRandomFunnels(initialPopulationSize = 500, selfingGenerations = 6, intercrossingGenerations = 1, nSeeds = 1)
pedigrees[[2]] <- fourParentPedigreeSingleFunnel(initialPopulationSize = 500, selfingGenerations = 6, intercrossingGenerations = 1, nSeeds = 1)
for(pedigree in pedigrees)
{
pedigree@selfing <- "infinite"
testFunc(map, pedigree)
}
})
test_that("Test non-zero generations of intercrossing",
{
testFunc <- function(map, pedigree)
{
#First check that with fully informative markers we get back the original data.
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane) + removeHets()
mapped <- new("mpcrossMapped", cross, map = map)
suppressWarnings(result <- computeGenotypeProbabilities(mapped))
genotypesFromProbabilities <- lapply(1:nLines(result), function(x)
{
apply(result@geneticData[[1]]@probabilities@data[(4*x-3):(4*x),], 2, which.max)
})
genotypesFromProbabilities <- do.call(rbind, genotypesFromProbabilities)
#The most probable founders should agree with the actual data, except for the case where the line really is hetrozygous.
expect_true(all((genotypesFromProbabilities == result@geneticData[[1]]@finals) | is.na(result@geneticData[[1]]@finals)))
}
map <- qtl::sim.map(len = c(100, 100), n.mar = 101, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
pedigrees <- list()
pedigrees[[1]] <- fourParentPedigreeRandomFunnels(initialPopulationSize = 500, selfingGenerations = 6, nSeeds = 1, intercrossingGenerations = 1)
pedigrees[[2]] <- fourParentPedigreeRandomFunnels(initialPopulationSize = 500, selfingGenerations = 6, nSeeds = 1, intercrossingGenerations = 2)
pedigrees[[3]] <- fourParentPedigreeSingleFunnel(initialPopulationSize = 500, selfingGenerations = 6, nSeeds = 1, intercrossingGenerations = 1)
pedigrees[[4]] <- fourParentPedigreeSingleFunnel(initialPopulationSize = 500, selfingGenerations = 6, nSeeds = 1, intercrossingGenerations = 2)
for(pedigree in pedigrees)
{
pedigree@selfing <- "infinite"
testFunc(map, pedigree)
}
})
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