context("Test similarity_by_set and similarity functions")
test_that("similarity_by_set returns correct values", {
expect_equal(similarity_by_set(gene_sets1 = list(c(1, 0, 1, 0, 1, 1, 0, 0), c(1, 1, 1, 0, 0, 0), c(1, 1, 1, 1, 1, 1), c(0, 0, 0), c(1, 1, 1), c(1, 1, 1), c(1, 0, 0)),
gene_sets2 = list(c(1, 1, 0, 0, 0, 1, 1, 0), c(0, 0, 0, 1, 1, 1), c(1, 1, 1, 0, 0, 0), c(0, 0, 0), c(0, 0, 0), c(1, 1, 1), c(1, 0, 0))),
data.frame(gene_set = c(1:7), index = c(0.5, 0, 0.5, 1, 0, 1, 1), set_size = c(8, 6, 6, 3, 3, 3, 3), in_genome1 = c(4, 3, 6, 0, 3, 3, 1), in_genome2 = c(4, 3, 3, 0, 0, 3, 1),
in_both = c(6, 6, 6, 0, 3, 3, 1)))
})
data("families_Bf")
sets_Bf = set_representation(families = families_Bf, gene_sets = reference_gene_sets)
test_that("similarity returns correct value", {
expect_equal(similarity(gene_sets1 = list(c(1, 1, 1, 1, 1, 1, 1, 1), c(1, 1, 1, 1, 1, 1)),
gene_sets2 = list(c(0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, 0, 0, 0, 0)),
threshold = 0.05, size = 1), 0)
expect_equal(similarity(gene_sets1 = list(c(0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, 0, 0, 0, 0)),
gene_sets2 = list(c(1, 1, 1, 1, 1, 1, 1, 1), c(1, 1, 1, 1, 1, 1)),
threshold = 0.05, size = 1), 0)
expect_equal(similarity(gene_sets1 = list(c(1, 0, 1, 0, 1, 1, 0, 0), c(1, 1, 1, 0, 0, 0), c(1, 1, 1, 1, 1, 1), c(0, 0, 0), c(1, 1, 1), c(1, 1, 1), c(1, 0, 0)),
gene_sets2 = list(c(1, 1, 0, 0, 0, 1, 1, 0), c(0, 0, 0, 1, 1, 1), c(1, 1, 1, 0, 0, 0), c(0, 0, 0), c(0, 0, 0), c(1, 1, 1), c(1, 0, 0)),
threshold = 0.05, size = 1), 0.5)
expect_equal(similarity(gene_sets1 = sets_Bf,
gene_sets2 = sets_Bf, threshold = 0.05, size = 4), 1)
})
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