Nothing
context("SegSites Class")
test_that("normal initialization of segsites works", {
snps <- matrix(c(1, 1, 0, 0, 1, 0, 0, 1, 1), 3, 3)
pos <- c(.1, .3, .5)
segsites <- create_segsites(snps, pos)
expect_true(is_segsites(segsites))
expect_equal(dim(segsites), c(3, 3))
expect_equal(nrow(segsites), 3)
expect_equal(ncol(segsites), 3)
expect_equal(get_positions(segsites), pos)
expect_equal(get_trio_locus(segsites), c(0, 0, 0))
expect_error(create_segsites(snps, 1:4 / 10))
expect_error(create_segsites(snps, pos, 1:4 / 10))
})
test_that("fixed positions are removed on initialization", {
snps <- matrix(c(1, 1, 0, 1, 1, 1, 0, 0, 0), 3, 3)
segsites <- create_segsites(snps, 1:3 / 10)
expect_equal(dim(segsites), c(3, 1))
expect_equal(get_positions(segsites), 0.1)
expect_equivalent(as.matrix(segsites), matrix(c(1, 1, 0), 3, 1))
})
test_that("subsetting of segsites works", {
segsites <- create_segsites(matrix(c(1, 1, 0, 1, 1,
0, 0, 0, 1, 0,
0, 1, 1, 0, 1), 3, 5, byrow = TRUE),
c(.1, .2, .5, .7, .75))
expect_equal(dim(segsites), c(3, 5))
ss_subset <- segsites[, 1:2]
expect_equal(dim(ss_subset), c(3, 2))
expect_equivalent(as.matrix(ss_subset), as.matrix(segsites)[, 1:2])
expect_equal(get_positions(ss_subset), get_positions(segsites)[1:2])
expect_equal(dim(segsites[, 1]), c(3, 1))
expect_equal(dim(segsites[1:2, ]), c(2, 3))
expect_equal(dim(segsites[-2, 1:3]), c(2, 2))
})
test_that("segsites can be converted to ms-output", {
segsites <- create_test_segsites()
output <- conv_to_ms_output(segsites)
expect_equal(output, c("segsites: 5",
"positions: 0.10 0.20 0.50 0.70 0.75",
"11011",
"00010",
"01101"))
})
test_that("converting segsites to matrix works", {
x <- create_test_segsites()
mat <- as.matrix(x)
expect_true(is.matrix(mat))
expect_false(is_segsites(mat))
})
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.