context("Test that lineWeights argument works")
test_that("Checking that value of lineWeights option doesn't change results for f2",
{
map <- qtl::sim.map(len = 100, n.mar = 11, anchor.tel=TRUE, include.x=FALSE, eq.spacing=TRUE)
f2Pedigree <- f2Pedigree(50)
nReps <- 4
for(i in 1:nReps)
{
cross <- simulateMPCross(map=map, pedigree=f2Pedigree, mapFunction = haldane)
allOneLineWeights <- estimateRF(subset(cross, lines = 1:49), keepLod = TRUE, keepLkhd = TRUE)
differentLineWeights <- estimateRF(cross, lineWeights = c(rep(1, 49), 0), keepLod = TRUE, keepLkhd = TRUE)
expect_identical(allOneLineWeights@rf@theta, differentLineWeights@rf@theta)
expect_equal(allOneLineWeights@rf@lod, differentLineWeights@rf@lod)
expect_equal(allOneLineWeights@rf@lkhd, differentLineWeights@rf@lkhd)
}
})
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