Nothing
context('pedigree methods')
test_that('pre-process pedigree',
{
data(samplePedigrees)
ped <- samplePedigrees$firstCousinPair
procPed <- processPedigree(ped)
expect_equal(procPed$ped, ped)
expect_equal(procPed$parents[,1], c(0,0))
expect_equal(procPed$parents[,2], c(0,0))
expect_equal(procPed$parents[,3], c(1,2))
expect_equal(procPed$parents[,5], c(1,2))
expect_equal(procPed$parents[,7], c(3,4))
expect_equal(procPed$parents[,8], c(5,6))
expect_equal(procPed$founders, c(1,2,4,6))
expect_equal(procPed$affected, c(7,8))
expect_equal(procPed$size, 8)
expect_equal(procPed$carriers, c(7,8))
expect_equal(procPed$id, 1:8)
expect_equal(procPed$finalDescendants, c(7,8))
})
test_that('pedigree calculations',
{
data(samplePedigrees)
ped <- samplePedigrees$firstCousinPair
procPed <- processPedigree(ped)
# descendants
expect_true(isDescendant(procPed, 1, 7))
expect_true(isDescendant(procPed, 2, 8))
expect_true(!isDescendant(procPed, 2, 4))
expect_true(!isDescendant(procPed, 3, 5))
expect_true(!isDescendant(procPed, 3, 8))
# mating
expect_true(areMating(procPed, 1, 2))
expect_true(areMating(procPed, 3, 4))
expect_true(!areMating(procPed, 2, 4))
expect_true(!areMating(procPed, 3, 5))
expect_true(!areMating(procPed, 6, 2))
# distance
expect_equal(ancestorDistance(procPed, 1, 3), 1)
expect_equal(ancestorDistance(procPed, 2, 7), 2)
expect_equal(ancestorDistance(procPed, 1, 5), 1)
expect_equal(ancestorDistance(procPed, 2, 8), 2)
expect_error(ancestorDistance(procPed, 1, 6))
expect_error(ancestorDistance(procPed, 5, 6))
expect_error(ancestorDistance(procPed, 8, 6))
expect_error(ancestorDistance(procPed, 1, 2))
})
test_that('kinship coefficient estimation',
{
data(samplePedigrees)
coefMatrix <- ComputeKinshipPropCoef(samplePedigrees$firstCousinPair)
expect_equal(unname(coefMatrix[1,]), c( NA, 0.875))
expect_equal(unname(coefMatrix[2,]), c(0.875, NA))
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.