Sys.setenv("R_TESTS" = "")
library(atacr)
context("summary and count functions")
test_that("target_count_summary() returns proper dataframe", {
smry <- target_count_summary(sim_counts)
expect_is(smry, "data.frame") #right class
expect_vectors_equal(colnames(smry), c("sample","percent_on_target", "on_target", "off_target"))
})
test_that("coverage_count_summary() returns proper dataframe", {
smry <- coverage_count_summary(sim_counts)
expect_is(smry, "data.frame")
expect_vectors_equal(colnames(smry), c("on_target", "off_target", "sample"))
})
test_that("target_count_coverage() returns proper dataframe", {
cov <- target_count_coverage(sim_counts)
expect_is(cov, "data.frame")
expect_vectors_equal(colnames(cov), c("sample", "target", "count_sum", "mean_coverage"))
})
test_that("target_count_coverage() returns proper sized dataframe", {
cov <- target_count_coverage(sim_counts)
expect_length(cov$count_sum, 12)
expect_equal(nrow(cov[cov$target == "on_target",]), 6)
expect_equal(nrow(cov[cov$target == "off_target",]), 6)
})
test_that("target_count_coverage() returns proper values in dataframe", {
cov <- target_count_coverage(sim_counts)
expect_vectors_equal(cov$count_sum,c(15001.00,15170.00,14976.00,16665.77,16755.63,16640.31,355.00,359.00,360.00,364.00,405.00,376.00))
})
test_that("sample_kmeans() returns proper dataframe and proper values in the dataframe", {
k <- sample_kmeans_cluster(sim_counts)
expect_vectors_equal(colnames(k), c("cluster_id", "sample"))
expect_vectors_equal(k$cluster_id, c(1,1,1,2,2,2))
})
test_that("count_windows_under_threshold() returns proper dataframe with proper values", {
th <- count_windows_under_threshold(sim_counts, threshold=15)
expect_vectors_equal(colnames(th), c("count", "threshold", "sample"))
expect_vectors_equal(th$count, c(0,0,0,4,4,4))
})
test_that("calc_quantiles() returns list() when threshold == NULL", {
l <- calc_quantiles(sim_counts)
expect_is(l, "list")
expect_has_all_and_only_these_members(l, c("bait_windows", "non_bait_windows"))
})
test_that("get_expected_values() returns right random numbers",{
set.seed(1234)
expect_vectors_equal(get_expected_values(c(1,2,3,4,1,2,3,4),dist="norm"),c(1.057280,2.831591,3.796155,-0.303645,3.012902,3.104852,1.813054,1.846650))
})
test_that("observed_expected_bins() gives right values", {
l <- observed_expected_bins(c(1,2,3,4,1,2,3,4))
expect_has_all_and_only_these_members(l, c("observed", "expected"))
expect_vectors_equal(l$observed, c(8))
expect_vectors_equal(l$expected, c(8))
})
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