context("Founder imputation isn't implemented for improper funnels (funnels with repeated founders)")
test_that("Eight parent design",
{
testFunc <- function(pedigree, map)
{
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane)
mapped <- new("mpcrossMapped", cross, map = map)
expect_error(result <- imputeFounders(mapped, errorProb = 0.1))
expect_error(result <- computeGenotypeProbabilities(mapped, errorProb = 0.1))
}
map1 <- qtl::sim.map(len = 100, n.mar = 201, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
map2 <- qtl::sim.map(len = c(100, 100), n.mar = 201, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
maps <- list(map1, map2)
pedigree1 <- eightParentPedigreeImproperFunnels(initialPopulationSize = 500, selfingGenerations = 10, nSeeds = 1)
pedigree1@selfing <- "infinite"
pedigree2 <- eightParentPedigreeImproperFunnels(initialPopulationSize = 500, selfingGenerations = 10, nSeeds = 1)
pedigree2@selfing <- "infinite"
pedigree3 <- eightParentPedigreeImproperFunnels(initialPopulationSize = 500, selfingGenerations = 5, nSeeds = 1)
pedigree3@selfing <- "finite"
pedigree4 <- eightParentPedigreeImproperFunnels(initialPopulationSize = 500, selfingGenerations = 5, nSeeds = 1)
pedigree4@selfing <- "finite"
pedigrees <- list(pedigree1, pedigree2, pedigree3, pedigree4)
for(map in maps)
{
for(pedigree in pedigrees)
{
testFunc(pedigree, map)
}
}
})
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