Nothing
skip_if_not_installed("kernlab")
data(hgsc)
hgsc <- hgsc[1:40, 1:30]
E <- consensus_cluster(hgsc, nk = 4, reps = 5,
algorithms = c("hc", "km", "sc"), progress = FALSE)
E_imputed <- impute_missing(E, hgsc, nk = 4)
test_that("adding majority vote elimnates all missing values", {
E_complete <- E_imputed
expect_equal(sum(is.na(E_complete)), 0)
expect_equal(nrow(E_complete), dim(E)[1])
expect_equal(ncol(E_complete), prod(dim(E)[2], dim(E)[3]))
})
test_that("errors thrown with incorrect inputs", {
expect_error(impute_missing(E, hgsc[-1, ]))
expect_error(impute_missing(E = sample(1:489), data = hgsc))
expect_error(impute_missing(E = E, data = as.data.frame(hgsc)))
})
test_that("majority completion not performed for a single assignment", {
E1 <- consensus_cluster(hgsc, nk = 4, reps = 1, algorithms = "hc",
progress = FALSE)
expect_equal(ncol(impute_missing(E1, hgsc, nk = 4)), 1)
})
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