Nothing
context("estimateRF vs estimateRFSingle, 8-parent tests")
test_that("Test actual maps",
{
testFunc <- function(pedigree, map)
{
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane) + multiparentSNP(keepHets = TRUE)
suppressWarnings(capture.output(rf1 <- estimateRF(cross)))
suppressWarnings(capture.output(rf2 <- mpMap2:::estimateRFSingleDesign(cross)))
expect_identical(rf1, rf2)
}
map1 <- qtl::sim.map(len = 100, n.mar = 11, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
map2 <- qtl::sim.map(len = c(100, 100), n.mar = 11, anchor.tel = TRUE, include.x=FALSE, eq.spacing=TRUE)
maps <- list(map1, map2)
pedigree1 <- eightParentPedigreeRandomFunnels(initialPopulationSize = 100, selfingGenerations = 10, nSeeds = 1, intercrossingGenerations = 0)
pedigree1@selfing <- "infinite"
pedigree2 <- eightParentPedigreeSingleFunnel(initialPopulationSize = 100, selfingGenerations = 10, nSeeds = 1, intercrossingGenerations = 0)
pedigree2@selfing <- "infinite"
pedigrees <- list(pedigree1, pedigree2)
for(map in maps)
{
for(pedigree in pedigrees)
{
testFunc(pedigree, map)
}
}
})
test_that("Using randomly chosen funnels, with finite generations of selfing",
{
distances <- c(1, 5)
for(intercrossingGenerations in 0:1)
{
for(selfingGenerations in 0:1)
{
pedigree <- eightParentPedigreeRandomFunnels(initialPopulationSize=100, selfingGenerations = selfingGenerations, intercrossingGenerations = intercrossingGenerations, nSeeds = 1)
pedigree@selfing <- "finite"
for(distance in distances)
{
map <- list("chr1" = c("a" = 0, "b" = distance))
class(map)<- "map"
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane)
#Ignore the warning about residual hetrozygosity
capture.output(rfSingle <- estimateRFSingleDesign(cross, recombValues = c(haldaneToRf(distance), (0:100)/200), keepLod = TRUE, keepLkhd=TRUE))
capture.output(rf <- estimateRF(cross, recombValues = c(haldaneToRf(distance), (0:100)/200), keepLod = TRUE, keepLkhd=TRUE))
expect_identical(rfSingle, rf)
expect_identical(rf@rf@theta[1,2], rf@rf@theta[2,1])
expect_identical(rf@rf@theta[1,1], 0)
expect_identical(rf@rf@theta[2,2], 0)
}
}
}
})
test_that("Using randomly chosen funnels, with infinite generations of selfing",
{
distances <- c(1, 5)
for(intercrossingGenerations in 0:1)
{
pedigree <- eightParentPedigreeRandomFunnels(initialPopulationSize=100, selfingGenerations = 6, intercrossingGenerations = intercrossingGenerations, nSeeds = 1)
pedigree@selfing <- "infinite"
for(distance in distances)
{
map <- list("chr1" = c("a" = 0, "b" = distance))
class(map)<- "map"
cross <- simulateMPCross(map=map, pedigree=pedigree, mapFunction = haldane) + removeHets()
#Ignore the warning about residual hetrozygosity
capture.output(rfSingle <- estimateRFSingleDesign(cross, recombValues = c(haldaneToRf(distance), (0:100)/200), keepLod = TRUE, keepLkhd=TRUE))
capture.output(rf <- estimateRF(cross, recombValues = c(haldaneToRf(distance), (0:100)/200), keepLod = TRUE, keepLkhd=TRUE))
expect_identical(rfSingle, rf)
expect_identical(rf@rf@theta[1,2], rf@rf@theta[2,1])
expect_identical(rf@rf@theta[1,1], 0)
expect_identical(rf@rf@theta[2,2], 0)
}
}
})
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