Nothing
context("SumStat SegSites")
test_that("SegSites statistic works", {
stat <- sumstat_seg_sites("segsites_test")
seg_sites <- list(create_segsites(matrix(c(1, 0, 0, 0,
1, 1, 0, 1,
1, 0, 0, 1,
1, 0, 0, 1), 4, 4, byrow = TRUE),
c(0.1, 0.2, 0.5, 0.7)))
expect_equal(stat$get_name(), "segsites_test")
expect_equal(stat$calculate(seg_sites, NULL, NULL), seg_sites)
})
test_that("SegSites are convert for trios", {
seg_sites <- list(create_segsites(matrix(c(1, 0, 0, 0, 1, 0, 0, 0, 0,
1, 1, 0, 1, 1, 1, 0, 1, 1,
0, 0, 1, 1, 0, 0, 1, 1, 1,
1, 0, 0, 1, 1, 0, 0, 1, 0),
4, 9, byrow = TRUE), 1:9 / 10))
expect_equal(conv_for_trios(seg_sites, coal_model(4) + locus_single(100)),
seg_sites)
model <- coal_model(4) + locus_trio(c(25, 30, 25), c(10, 10))
seg_sites_trio <- seg_sites
seg_sites_trio[[1]] <- create_segsites(get_snps(seg_sites_trio[[1]][ , c(1:2, 4:6, 8:9)]), #nolint
c(.4, 0.8, c(5, 15, 25) / 30, .2, .6),
c(-1, -1, 0, 0, 0, 1, 1))
expect_equal(conv_for_trios(seg_sites, model), seg_sites_trio)
seg_sites <- list(seg_sites[[1]], seg_sites[[1]])
seg_sites_trio <- list(seg_sites_trio[[1]], seg_sites_trio[[1]])
# Two loci groups
model <- model + locus_trio(c(25, 30, 25), c(10, 10))
expect_equal(conv_for_trios(seg_sites, model), seg_sites_trio)
# Multiple loci in a group
model <- coal_model(4) + locus_trio(c(25, 30, 25), c(10, 10), number = 2)
expect_equal(conv_for_trios(seg_sites, model), seg_sites_trio)
})
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