test_that("the RC-Exclusivity test works", {
library(dplyr)
dat <- tibble::tribble(
~samples, ~genes,
"A", "gene1",
"A", "gene2",
"B", "gene1",
"B", "gene3",
"C", "gene3"
)
k <- 2
N_perms <- 6
expect_error(rc_test(dat, samples, genes, which_test = "fake_test"),
regexp = "is not an option.")
rc_res <- rc_test(dat, samples, genes,
k = k,
which_test = "exclusivity",
N_perms = N_perms,
min_mut_events = 0,
min_times_mut = 0)
expect_true(tibble::is_tibble(rc_res))
expect_true(ncol(rc_res) == 4)
gene_sets <- rc_res$gene_sets
lengths <- purrr::map_lgl(gene_sets, ~ length(.x) == 2)
expect_true(all(lengths))
expect_equal(unlist(rc_res$t_AM), c(1, 2, 3))
pval_check <- rc_res %>%
mutate(pval_check = (t_BM_ge / !!N_perms) == p_val) %>%
pull(pval_check) %>%
unlist()
expect_true(all(pval_check))
})
test_that("the RC-Co-mutation test works", {
library(dplyr)
dat <- tibble::tribble(
~samples, ~genes,
"A", "gene1",
"A", "gene2",
"B", "gene1",
"B", "gene3",
"C", "gene3"
)
k <- 2
N_perms <- 6
expect_error(rc_test(dat, samples, genes, which_test = "fake_test"),
regexp = "is not an option.")
rc_res <- rc_test(dat, samples, genes,
k = k,
which_test = "comutation",
N_perms = N_perms,
min_mut_events = 0,
min_times_mut = 0)
expect_true(tibble::is_tibble(rc_res))
expect_true(ncol(rc_res) == 4)
gene_sets <- rc_res$gene_sets
lengths <- purrr::map_lgl(gene_sets, ~ length(.x) == 2)
expect_true(all(lengths))
expect_equal(unlist(rc_res$t_AM), c(1, 1))
pval_check <- rc_res %>%
mutate(pval_check = (t_BM_ge / !!N_perms) == p_val) %>%
pull(pval_check) %>%
unlist()
expect_true(all(pval_check))
})
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